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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acacaccaacttaaatactcttgggagtcccaggatcatgctaatttcaaaacacttgtcacctcttagaccgaatggtttctttaaccgagacattcagACAAGAAGAATGAGAACAAGGAGGTTGCTGTCAATGACTTCCTGCCTGCAAGTGCTGCTTATGAGGCCATAAAGCACTCCAT

Basic information

species Oryza sativa
transcript LOC_Os05g02310.1
intron # 7
splice site 3'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g02310.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G137930_T02 (Zea mays), 3'ss of exon 7
---acacaccaacttaaatactcttgggagtcccaggatcatgctaatttcaaaacacttgtcacctcttagaccgaatggtttctttaaccgagacattcagACAAGAAGAATGAGAACAAGGAGGTTGCTGTCAATGACTTCCTGCCTGCAAGTGCTGCTTATGAGGCCATAAAGCACTCCAT
   | | |||   | |  |  | ||     ||  | ||   ||  ||| | |     |||| | ||| |||||  ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||| || || || || || |||||||| |||||| ||||||| ||
gagaaaaacctg-tcaggtgtttttaactctcttaagacggtgtaaatgttag--tgcttgcctcctgttagattgaatggtttctttaaccgagacattcagACAAGAAGAATGAGAACAAGGAGGTTGCTGTGAATGACTTTCTACCAGCGAGCGCCGCTTATGAAGCCATACAGCACTCTAT

upper sequence: LOC_Os05g02310.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA13G19500.2 (Glycine max), 3'ss of exon 7
acacaccaacttaaatactcttgggagtcccaggatcatgctaatttcaaaacacttgtcacctcttagaccgaatggtttctttaaccgagacattcagACAAGAAGAATGAGAACAAGGAGGTTGCTGTCAATGACTTCCTGCCTGCAAGTGCTGCTTATGAGGCCATAAAGCACTCCAT
       | | |  | |     | ||    ||  |  ||  |  |       ||  |   | |            || |||  ||||   ||  ||| |||||||||||||||||||||||| ||||| || || ||||| || |||||    ||||| ||||| || || ||||| |||||
----gttagcatctacataacagcgaaatacacaagtatcatt-tggtgcgccatgtaaaatcaaactatttttgtgtttttcttaataaagGAATT-AGACAAGAAGAATGAGAACAAGGAAGTTGCAGTGAACGACTTTCTTCCTGCCTCAGCTGCCTATGAAGCGATCAAGCATTCCAT

upper sequence: LOC_Os05g02310.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA13G19500.1 (Glycine max), 3'ss of exon 7
-------------------------------acacaccaacttaaatactcttgggagtcccaggatcatgctaatttcaa--aacacttgtcacctctt---agaccgaa---------tggtttctttaaccgagacattcagACAAGAAGAATGAGAACAAGGAGGTTGCTGTCAATGACTTCCTGCCTGCAAGTGCTGCTTATGAGGCCATAAAGCACTCCAT
                                  || ||  |   ||| | || | |    ||  |    |  |    |||  | || |||   |  | |   | | | ||         || |||  ||||   ||  ||| |||||||||||||||||||||||| ||||| || || ||||| || |||||    ||||| ||||| || || ||||| |||||
gtatcctttccaagaatttcaaaatgtgtttgttcagcacttcctata-tgttagcatctacataacagcgaaatacacaagtatcatttggtgcgccatgtaaaatcaaactatttttgtgtttttcttaataaaggaatt-agACAAGAAGAATGAGAACAAGGAAGTTGCAGTGAACGACTTTCTTCCTGCCTCAGCTGCCTATGAAGCGATCAAGCATTCCAT

upper sequence: LOC_Os05g02310.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA10G05130.1 (Glycine max), 3'ss of exon 7
-------------acacaccaacttaaatactcttgggagtcccaggatcatgctaatttca-----aaacacttgtcacctctta---gaccgaa--------tggtttctttaaccgagacattcagACAAGAAGAATGAGAACAAGGAGGTTGCTGTCAATGACTTCCTGCCTGCAAGTGCTGCTTATGAGGCCATAAAGCACTCCAT
               |   |||  |   |    |  | | | ||   ||  |   |  |  |     || || ||| |    | ||    | | ||        || |||| ||||   ||  ||| |||||||||||||||||||||||| ||||| || || ||||| || |||||    ||||| ||||| || || ||||| |||||
gtatcctttccaagaatttcaaaatgtgtttgttcagtacttcctatatgttagcatctatataggtaatcatttggcgtgccatataaaatcaaactattttatgttttccttaataaaggaatt-agACAAGAAGAATGAGAACAAGGAAGTTGCAGTGAACGACTTTCTTCCTGCTTCAGCTGCCTATGAAGCTATCAAGCATTCCAT

upper sequence: LOC_Os05g02310.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv08s0040g02470.t01 (Vitis vinifera), 3'ss of exon 7
---------------------------------------------------------acacaccaacttaaatactcttgggagtcccaggatcatgctaatttcaaaacacttgtcacctcttagaccgaatggtttctttaaccgagacattcagACAAGAAGAATGAGAACAAGGAGGTTGCTGTCAATGACTTCCTGCCTGCAAGTGCTGCTTATGAGGCCATAAAGCACTCCAT
                                                          || ||   | | || |  ||||    |      || ||   || |  | || | | |     ||| |  |    |  |||   | |   |  || ||||||||||| |||||||||||||| ||||| || || ||||| |||||  |      |||||||||||| ||  |||| |||||
gtatccttctaaaaattcttaatccttagcaaacactagtttaaaacgattcttcaagcatactgtccttaaaatacttgtttatttttttataatctcaaatctagaaaattgg----atctaaatcatcctttttttccttaataaaccaatcagACAAGAAAAATGAGAACAAGGAAGTTGCAGTTAACGACTTTCTGCCATCTTCCAGTGCTTATGAGGCAATCCAGCATTCCAT

upper sequence: LOC_Os05g02310.1 (Oryza sativa), 3'ss of exon 7
lower sequence: PP1S315_67V6.1 (Physcomitrella patens), 3'ss of exon 4
-------------------------------acacaccaacttaa-atactcttgggagtcccaggatcatgctaatttcaaaacacttgtcacctcttagaccgaatggtttctttaaccgagacattcagACAAGAAGAATGAGAACAAGGAGGTTGCTGTCAATGACTTCCTGCCTGCAAGTGCTGCTTATGAGGCCATAAAGCACTCCAT
                                || |       || ||      | |||     |     |  |   ||      |  ||| || | |   ||||   ||  |   |    | |  | |||||||||||||||||||||||||| ||  | ||  || ||||||||         |||||   | | ||||| |  ||||||||
gtaagtgccgagtgaggtgacgcggtgatgtgcataatggtccaagatgtggacgtgagagagggaggtgtctttgcttgtggtgatgtgtgacgtttgtaaccggcagggatgggtt-tggggtgaatcagACAAGAAGAATGAGAACAAGGAAGTAACGGTGGATAACTTCCTGGGCCACGAAGCTGCGATTCAAGCCATCAGTCACTCCAT

upper sequence: LOC_Os05g02310.1 (Oryza sativa), 3'ss of exon 7
lower sequence: PP1S552_1V6.1 (Physcomitrella patens), 3'ss of exon 7
-------------------------------acacaccaacttaa-atactcttgggagtcccaggatcatgctaatttcaaaacacttgtcacctcttagaccgaatggtttctttaaccgagacattcagACAAGAAGAATGAGAACAAGGAGGTTGCTGTCAATGACTTCCTGCCTGCAAGTGCTGCTTATGAGGCCATAAAGCACTCCAT
                                || |       || ||      | |||    ||     |  |   ||      |  ||| || | |   ||||   ||  |   |    | |  | |||||||||||||||||||||||||| ||  | ||  || ||||||||         |||||   | | ||||| |  ||||||||
gtaagtgccgagtgaggtgacgcggtgatgtgcataatggtccaagatgtggacgtgagagagagaggtgtctttgcttgtggtgatgtgtgacgtttgtaaccggcagggatgggtt-tggggtgaatcagACAAGAAGAATGAGAACAAGGAAGTAACGGTGGATAACTTCCTGGGCCACGAAGCTGCGATTCAAGCCATCAGTCACTCCAT

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|88487192|gb|CI424463.1|CI424463
EST:     CCTCACCGCTTGGCTGAAATCAGGCGCTTTTTTGAGGACT                         ACAAGAAGAATGAGAACAAGGAGGTTGCTGTCAATGACTTCCTGCCTGCAA
genomic: CCTCACCGCTTGGCTGAAATCAGGCGCTTTTTTGAGGACTgtatcctttt ... agacattcagACAAGAAGAATGAGAACAAGGAGGTTGCTGTCAATGACTTCCTGCCTGCAA
EST: gi|8859734|gb|AU097052.1|AU097052
EST:     GGAGCTCCCACCTCACCGNTTGGCTGAAANCAGGCGCTTTTTTGAGGACT                         ACAAGAAGAATGAGAACAAGGAGGTTGCTGTCAATGACTTCCTGCCTGCAA
genomic: GGAGCTCCCACCTCACCGCTTGGCTGAAATCAGGCGCTTTTTTGAGGACTgtatcctttt ... agacattcagACAAGAAGAATGAGAACAAGGAGGTTGCTGTCAATGACTTCCTGCCTGCAA
EST: gi|88215769|gb|CI215618.1|CI215618
EST:     GGAGCTCCCACCTCACCGCTTGGCTGAAATCAGGCGCTTTTTTGAGGACT                         ACAAGAAGAATGAGAACAAGGAGGTTGCTGTCAATGACTTCCTGCCTGCAA
genomic: GGAGCTCCCACCTCACCGCTTGGCTGAAATCAGGCGCTTTTTTGAGGACTgtatcctttt ... agacattcagACAAGAAGAATGAGAACAAGGAGGTTGCTGTCAATGACTTCCTGCCTGCAA
EST: gi|2311572|gb|C27727.1|C27727
EST:     GGAGCTCCCACCTCACCGCTTGGCTGAAATCAGGCGCTTTTTTNAGGACT                         ACAAGAAGAATGAGAACAAGGAGGTTGCTGTCAATGACTTCCTGCCTGCAA
genomic: GGAGCTCCCACCTCACCGCTTGGCTGAAATCAGGCGCTTTTTTGAGGACTgtatcctttt ... agacattcagACAAGAAGAATGAGAACAAGGAGGTTGCTGTCAATGACTTCCTGCCTGCAA
EST: gi|86873320|gb|CI341545.1|CI341545
EST:     GGAGCTCCCACCTCACCGCTTGGCTGAAATCAGGCGCTTTTTTGAGGACT                         ACAAGAAGAATGAGAACAAGGAGGTTGCTGTCAATGACTTCCTGCCTGCAA
genomic: GGAGCTCCCACCTCACCGCTTGGCTGAAATCAGGCGCTTTTTTGAGGACTgtatcctttt ... agacattcagACAAGAAGAATGAGAACAAGGAGGTTGCTGTCAATGACTTCCTGCCTGCAA
EST: gi|86884666|gb|CI313045.1|CI313045
EST:     GGAGCTCCCACCTCACCGCTTGGCT-AAATCAGGCCCTTTTTTGA-GACT                         ACAAGAAGAATGAGAACAAGGAGGTTGCTGTCAATGACTTCCTGCCTGCAA
genomic: GGAGCTCCCACCTCACCGCTTGGCTGAAATCAGGCGCTTTTTTGAGGACTgtatcctttt ... agacattcagACAAGAAGAATGAGAACAAGGAGGTTGCTGTCAATGACTTCCTGCCTGCAA
EST: gi|88985884|gb|CI033213.1|CI033213
EST:     GCGCTTTTTTGAGGACT                         ACAAGAAGAATGAGAACAAGGAGGTTGCTGTCAATGACTTCCTGCCTGCAA
genomic: GCGCTTTTTTGAGGACTgtatcctttt ... agacattcagACAAGAAGAATGAGAACAAGGAGGTTGCTGTCAATGACTTCCTGCCTGCAA
EST: gi|88981027|gb|CI021154.1|CI021154
EST:     GGAGCTCCCACCTCACCGCTTGGCTGAAATCAGGCGCTTTTTTGAGGACT                         ACAAGAAGAATGAGAACAAGGAGGTTGCTGTCAATGACTTCCTGCCTGCAA
genomic: GGAGCTCCCACCTCACCGCTTGGCTGAAATCAGGCGCTTTTTTGAGGACTgtatcctttt ... agacattcagACAAGAAGAATGAGAACAAGGAGGTTGCTGTCAATGACTTCCTGCCTGCAA
EST: gi|8594726|gb|AU093264.1|AU093264
EST:     GGAGCTCCCACCTCACCGCTTGGCTGAAATCAGGCGCTTTTTTGAGGACT                         ACAAGAAGAATGAGAACAAGGAGGTTGCTGTCAATGACTTCCTGCCTGCAA
genomic: GGAGCTCCCACCTCACCGCTTGGCTGAAATCAGGCGCTTTTTTGAGGACTgtatcctttt ... agacattcagACAAGAAGAATGAGAACAAGGAGGTTGCTGTCAATGACTTCCTGCCTGCAA
EST: gi|88543309|gb|CI473307.1|CI473307
EST:     GGAGCTCCCACCTCACCGCTTGGCTGAAATCAGGCGCTTTTTTGAGGACT                         ACAAGAAGAATGAGAACAAGGAGGTTGCTGTCAATGACTTCCTGCCTGCAA
genomic: GGAGCTCCCACCTCACCGCTTGGCTGAAATCAGGCGCTTTTTTGAGGACTgtatcctttt ... agacattcagACAAGAAGAATGAGAACAAGGAGGTTGCTGTCAATGACTTCCTGCCTGCAA
EST: gi|3761138|gb|C98386.1|C98386
EST:     GGAGCTCCCACCTCACCGCTTGGCTGAAATCAGGCGCTTTTTTGAGGACT                         ACAAGAAGAATGAGAACAAGGAGGTTGCTGTCAATGACTTCCTGCCTGCAA
genomic: GGAGCTCCCACCTCACCGCTTGGCTGAAATCAGGCGCTTTTTTGAGGACTgtatcctttt ... agacattcagACAAGAAGAATGAGAACAAGGAGGTTGCTGTCAATGACTTCCTGCCTGCAA
EST: gi|88959894|gb|CI381772.1|CI381772
EST:     TCACCGCTTGGCTTAAATCAGGCGCTTTTTTGAGGACT                         ACAAGAAGAATGAGAACAAGGAGGTTCCTGTCAATGACTTCCTGCCTGCAA
genomic: TCACCGCTTGGCTGAAATCAGGCGCTTTTTTGAGGACTgtatcctttt ... agacattcagACAAGAAGAATGAGAACAAGGAGGTTGCTGTCAATGACTTCCTGCCTGCAA
EST: gi|88259427|gb|CI363720.1|CI363720
EST:     GGAGCTCCCACCTCACCGCTTGGCTGAAATCAGGCGCTTTTTTGAGGACT                         ACAAGAAGAATGAGAACAAGGAGGTTGCTGTCAATGACTTCCTGCCTGCAA
genomic: GGAGCTCCCACCTCACCGCTTGGCTGAAATCAGGCGCTTTTTTGAGGACTgtatcctttt ... agacattcagACAAGAAGAATGAGAACAAGGAGGTTGCTGTCAATGACTTCCTGCCTGCAA
EST: gi|88275373|gb|CI395224.1|CI395224
EST:     GGAGCTCCCACCTCACCGCTTGGCTGAAATCAGGCGCTTTTTTGAGGACT                         ACAAGAAGAATGAGAACAAGGAGGTTGCTGTCAATGACTTCCTGCCTGCAA
genomic: GGAGCTCCCACCTCACCGCTTGGCTGAAATCAGGCGCTTTTTTGAGGACTgtatcctttt ... agacattcagACAAGAAGAATGAGAACAAGGAGGTTGCTGTCAATGACTTCCTGCCTGCAA
EST: gi|88525673|gb|CI452691.1|CI452691
EST:     AAATCAGGCGCTTTTTTGAGGACT                         ACAAGAAGAATGAGAACAAGGAGGTTGCTGTCAATGACTTCCTGCCTGCAA
genomic: AAATCAGGCGCTTTTTTGAGGACTgtatcctttt ... agacattcagACAAGAAGAATGAGAACAAGGAGGTTGCTGTCAATGACTTCCTGCCTGCAA
EST: gi|33663513|gb|CF294480.1|CF294480
EST:     GGAGCTCCCACCTCACCGCTTGGCTGAAATCAGGCGCTTTTTTGAGGACT                         ACAAGAAGAATGAGAACAAGGAGGTTGCTGTCAATGACTTCCTGCCTGCAA
genomic: GGAGCTCCCACCTCACCGCTTGGCTGAAATCAGGCGCTTTTTTGAGGACTgtatcctttt ... agacattcagACAAGAAGAATGAGAACAAGGAGGTTGCTGTCAATGACTTCCTGCCTGCAA
EST: gi|88237667|gb|CI237516.1|CI237516
EST:     GGAGCTCCCACCTCACCGCTTGGCTGAAATCAGGCGCTTTTTTGAGGACT                         ACAAGAAGAATGAGAACAAGGAGGTTGCTGTCAATGACTTCCTGCCTGCAA
genomic: GGAGCTCCCACCTCACCGCTTGGCTGAAATCAGGCGCTTTTTTGAGGACTgtatcctttt ... agacattcagACAAGAAGAATGAGAACAAGGAGGTTGCTGTCAATGACTTCCTGCCTGCAA
EST: gi|88537571|gb|CI466532.1|CI466532
EST:     CTTTTTTGAGGACT                         ACAAGAAGAATGAGAACAAGGAGGTTGCTGTCAATGACTTCCTGCCTGCAA
genomic: CTTTTTTGAGGACTgtatcctttt ... agacattcagACAAGAAGAATGAGAACAAGGAGGTTGCTGTCAATGACTTCCTGCCTGCAA
EST: gi|88533757|gb|CI460418.1|CI460418
EST:     GCTGAAATCAGGCGCTTTTTTGAGGACT                         ACAAGAAGAATGAGAACAAGGAGGTTGCTGTCAATGACTTCCTGCCTGCAA
genomic: GCTGAAATCAGGCGCTTTTTTGAGGACTgtatcctttt ... agacattcagACAAGAAGAATGAGAACAAGGAGGTTGCTGTCAATGACTTCCTGCCTGCAA
EST: gi|88542616|gb|CI471955.1|CI471955
EST:     AATCAGGCGCTTTTTTGAGGACT                         ACAAGAAGAATGAGAACAAGGAGGTTGCTGTCAATGACTTCCTGCCTGCAA
genomic: AATCAGGCGCTTTTTTGAGGACTgtatcctttt ... agacattcagACAAGAAGAATGAGAACAAGGAGGTTGCTGTCAATGACTTCCTGCCTGCAA
EST: gi|38482067|gb|CF966128.1|CF966128
EST:     GGAGCTCCCACCTCACCGCTTGGCTGAAATCAGGCGCTTTTTTGAGGACT                         ACAAGAAGAATGAGAACAAGGAGGTTGCTGTCAATGACTTCCTGCCTGCAA
genomic: GGAGCTCCCACCTCACCGCTTGGCTGAAATCAGGCGCTTTTTTGAGGACTgtatcctttt ... agacattcagACAAGAAGAATGAGAACAAGGAGGTTGCTGTCAATGACTTCCTGCCTGCAA
EST: gi|3763568|gb|AU030320.1|AU030320
EST:     GGAGCTCCCACCTCACCGCTTGGCTGAAATCAGGCGCTTTTTTGAGGACT                         ACAAGAAGAATGAGAACAAGGAGGTTGCTGTCAATGACTTCCTGCCTGCAA
genomic: GGAGCTCCCACCTCACCGCTTGGCTGAAATCAGGCGCTTTTTTGAGGACTgtatcctttt ... agacattcagACAAGAAGAATGAGAACAAGGAGGTTGCTGTCAATGACTTCCTGCCTGCAA
EST: gi|87039814|gb|CI194436.1|CI194436
EST:     GGAGCTCCCACCTCACCGCTTGGCTGAAATCAGGCGCTTTTTTGAGGACT                         ACAAGAAGAATGAGAACAAGGAGGTTGCTGTCAATGACTTCCTGCCTGCAA
genomic: GGAGCTCCCACCTCACCGCTTGGCTGAAATCAGGCGCTTTTTTGAGGACTgtatcctttt ... agacattcagACAAGAAGAATGAGAACAAGGAGGTTGCTGTCAATGACTTCCTGCCTGCAA
EST: gi|86842354|gb|CI335258.1|CI335258
EST:     GGAGCTCCCACCTCACCGCTTGGCTGAAATCAGGCGCTTTTTTGAGGACT                         ACAAGAAGAATGAGAACAAGGAGGTTGCTGTCAATGACTTCCTGCCTGCAA
genomic: GGAGCTCCCACCTCACCGCTTGGCTGAAATCAGGCGCTTTTTTGAGGACTgtatcctttt ... agacattcagACAAGAAGAATGAGAACAAGGAGGTTGCTGTCAATGACTTCCTGCCTGCAA
EST: gi|88544451|gb|CI472550.1|CI472550
EST:     GAGCTCCCACCTCACCGCTTGGCTGAAATCAGGCGCTTTTTTGAGGACT                         ACAAGAAGAATGAGAACAAGGA-GTTGGCTGTCAATGACTTCCTGCCTGCA
genomic: GAGCTCCCACCTCACCGCTTGGCTGAAATCAGGCGCTTTTTTGAGGACTgtatcctttt ... agacattcagACAAGAAGAATGAGAACAAGGAGGTT-GCTGTCAATGACTTCCTGCCTGCA
EST: gi|117243396|gb|CT843443.1|CT843443
EST:     GAGCTCCCACCTCACCGCTTGGCTGAAATCAGGCGCTTTTT-GAGGACCT                         ACA-GAAGAATGAGAACAAGGAGGTTGCTGTCAATGACTTCCTGCCTGCA
genomic: GAGCTCCCACCTCACCGCTTGGCTGAAATCAGGCGCTTTTTTGAGGAC-Tgtatcctttt ... agacattcagACAAGAAGAATGAGAACAAGGAGGTTGCTGTCAATGACTTCCTGCCTGCA
EST: gi|87039980|gb|CI194602.1|CI194602
EST:     GGAGCTCCCACCTCACCGCTTGGCTGAAATCAGGCGCTTTTTTGAGGACT                         ACAAGAAGAATGAGAACAAGGAGGTTGCTGTCAATGACTTCCTGCCTGCAA
genomic: GGAGCTCCCACCTCACCGCTTGGCTGAAATCAGGCGCTTTTTTGAGGACTgtatcctttt ... agacattcagACAAGAAGAATGAGAACAAGGAGGTTGCTGTCAATGACTTCCTGCCTGCAA
EST: gi|88537394|gb|CI465225.1|CI465225
EST:     TTTTGAGGACT                         ACAAGAAGAATGAGAACAAGGAGGTTGCTGTCAATGACTTCCTGCCTGCAA
genomic: TTTTGAGGACTgtatcctttt ... agacattcagACAAGAAGAATGAGAACAAGGAGGTTGCTGTCAATGACTTCCTGCCTGCAA
EST: gi|86883005|gb|CI314249.1|CI314249
EST:     -GAGCTCCCACCTCACCGCTTGGCTGAAATCAGGCGCTTTTTTGAGGACT                         ACAAGAAGAATGAG-ACAAGGAGGTTCCTGTCAATGACTTCCTGCCTGCAA
genomic: GGAGCTCCCACCTCACCGCTTGGCTGAAATCAGGCGCTTTTTTGAGGACTgtatcctttt ... agacattcagACAAGAAGAATGAGAACAAGGAGGTTGCTGTCAATGACTTCCTGCCTGCAA
EST: gi|86603118|gb|CI357482.1|CI357482
EST:     GGAGCTCCCACCTCACCCCTTGGCTGAAATCAGGCGCTTTTTTGAGGACT                         ACAAGAAGAATTAGAACAAGGAGGTTGCTGTCAATGACTTCCTGCCTCCAA
genomic: GGAGCTCCCACCTCACCGCTTGGCTGAAATCAGGCGCTTTTTTGAGGACTgtatcctttt ... agacattcagACAAGAAGAATGAGAACAAGGAGGTTGCTGTCAATGACTTCCTGCCTGCAA
EST: gi|8956900|gb|BE230703.1|BE230703
EST:     ATCAGGCGNTWTTTTGAGGACT                         ACAAGAAGAATGAGAACAAVANANGTTGCTGTCAATGACTTCCTGCCTGCA
genomic: ATCAGGCGCTTTTTTGAGGACTgtatcctttt ... agacattcagACAAGAAGAATGAGAACAA-GGAGGTTGCTGTCAATGACTTCCTGCCTGCA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 47 (upstream exon), 75 (downstream exon)
Score: 68

ATTGCCGTTTGTGCTGATGATCCTGAGTACAAGCATTACAATGATATCAAGGAGCTCCCACCTCACCGCTTGGCTGAAATCAGGCGCTTTTTTGAGGACTgtatcctttt ... agacattcagACAAGAAGAATGAGAACAAGGAGGTTGCTGTCAATGACTTCCTGCCTGCAAGTGCTGCTTATGAGGCCATAAAGCACTCCAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcaaaacacttgtcacctcttagaccgaatggtttctttaaccgagacattcagACAAGAAGAATGAGAACAAGGAGGTTGCTGTCAATGACTTCCTGCCTGCAAGTGCTGCTTATGAGGCCATAAAGCACTCCAT
                                  ttctttaac  putative branch site 
                                 tttctttaa  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acacaccaacttaaatactcttgggagtcccaggatcatgctaatttcaaaacacttgtcacctcttagaccgaatggtttctttaaccgagacattcagACAAGAAGAATGAGAACAAGGAGGTTGCTGTCAATGACTTCCTGCCTGCAAGTGCTGCTTATGAGGCCATAAAGCACTCCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- -caccaac
- - - - - - - - - - - - - - - - - - catgcta
- - - - - - - - - - - - - - - - - - - - - - - -caaaacac