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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcctttccaagaatttcaaaatgtgtttgttcagtacttcctatatgttagcatctatataggtaatcatttggcgtgccatataaaatcaaactattttatgttttccttaataaaggaattagACAAGAAGAATGAGAACAAGGAAGTTGCAGTGAACGACTTTCTTCCTGCTTCAGCTGCCTATGAAGCTATCAAGCATTCCAT

Basic information

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

upper sequence: GLYMA10G05130.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G137930_T02 (Zea mays), 3'ss of exon 7
gtatcctttccaagaatttcaaaatgtgtttgttcagtacttcctatatgttagcatctatataggtaatcatttggcgtgccatataaaatcaaactattttatgttttccttaataaaggaatt-agACAAGAAGAATGAGAACAAGGAAGTTGCAGTGAACGACTTTCTTCCTGCTTCAGCTGCCTATGAAGCTATCAAGCATTCCAT
                     | |      |||   ||  ||   |     |     |  | ||  |  | | |    |   | | | | ||  ||        || |||| ||||   ||  ||| |||||||||||||||||||||||| ||||| ||||| |||||||| || ||    || || |||||||| ||  |||| || ||
--------------------gagaaaaacctgtcaggtgtttttaactctcttaagacggtgtaaatg-ttagtgcttgcctcctgttagattgaa--------tggtttctttaaccgagacattcagACAAGAAGAATGAGAACAAGGAGGTTGCTGTGAATGACTTTCTACCAGCGAGCGCCGCTTATGAAGCCATACAGCACTCTAT

upper sequence: GLYMA10G05130.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv08s0040g02470.t01 (Vitis vinifera), 3'ss of exon 7
-------------------gtatcctttccaagaatt---tcaaaatgtgttt----gttcagtacttcctatatgttagcatctatataggtaatcatttggcgtgccatataaaatcaaactattttatgttttccttaataaaggaattagACAAGAAGAATGAGAACAAGGAAGTTGCAGTGAACGACTTTCTTCCTGCTTCAGCTGCCTATGAAGCTATCAAGCATTCCAT
                     ||||||  |||  | |   | |||| |  | |    |   | |       | ||  | |  | | | |   ||||| |      |   | ||   ||| || |  |   | ||||||||||||||  ||| ||||||||| ||||||||||||||||||||||| ||||||||||| ||  ||||   ||| ||||| || ||| ||||||||||
gtatccttctaaaaattcttaatccttagcaaacactagtttaaaacgattcttcaagcatactgtccttaaaatacttgtttatttttttataatc-tcaaatctagaaaattggatctaaatcatcctttttttccttaataaaccaatcagACAAGAAAAATGAGAACAAGGAAGTTGCAGTTAACGACTTTCTGCCATCTTCCAGTGCTTATGAGGCAATCCAGCATTCCAT

upper sequence: GLYMA10G05130.1 (Glycine max), 3'ss of exon 7
lower sequence: PP1S315_67V6.1 (Physcomitrella patens), 3'ss of exon 4
gtatcctttccaagaatttcaaaatgtgtttgttcagtact-tcctatatgttagcatctatataggtaatcatttggcgtgccatataaaatcaaactattttatgttttccttaa---taaag-gaattagACAAGAAGAATGAGAACAAGGAAGTTGCAGTGAACGACTTTCTTCCTGCTTCAGCTGCCTATGAAGCTATCAAGCATTCCAT
   |   | || ||       |   |    ||| ||  |   ||| | ||||   | |       ||   |   || || ||   |      | |   |  |    |       |     |   | |||| |||||||||||||||||||||||||||  | ||| |  |||| ||         ||||||   | |||| ||||  || |||||
--gtaagtgccgagtgaggtgacgcggtgatgtgcataatggtccaagatgtggacgtgagagagggaggtgtctttgcttgtggtgatgtgtgacgtttgtaaccggcagggatgggtttggggtgaatcagACAAGAAGAATGAGAACAAGGAAGTAACGGTGGATAACTTCCTGGGCCACGAAGCTGCGATTCAAGCCATCAGTCACTCCAT

upper sequence: GLYMA10G05130.1 (Glycine max), 3'ss of exon 7
lower sequence: PP1S552_1V6.1 (Physcomitrella patens), 3'ss of exon 7
gtatcctttccaagaatttcaaaatgtgtttgttcagtact-tcctatatgttagcatct---atataggtaa--tcatttggcgtgccatataaaatcaaactattttatgttttccttaataaaggaattagACAAGAAGAATGAGAACAAGGAAGTTGCAGTGAACGACTTTCTTCCTGCTTCAGCTGCCTATGAAGCTATCAAGCATTCCAT
   |   | || ||       |   |    ||| ||  |   ||| | ||||   | |     | | ||||    |   |||  |||   | | |  |           | |  |   ||       |||| |||||||||||||||||||||||||||  | ||| |  |||| ||         ||||||   | |||| ||||  || |||||
--gtaagtgccgagtgaggtgacgcggtgatgtgcataatggtccaagatgtggacgtgagagagagaggtgtctttgcttgtggtgatgtgtgacgtttgtaaccggcagggatgggtttg-gggtgaatcagACAAGAAGAATGAGAACAAGGAAGTAACGGTGGATAACTTCCTGGGCCACGAAGCTGCGATTCAAGCCATCAGTCACTCCAT

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|209704319|gb|BW683551.1|BW683551
EST:     GGACCTTCCTCCTCACCGTTTAGCTGAAATTCGTCGTTTCTTTGAAGATT                         ACAAGAAGAATGAGAACAAGGAAGTTGCAGTGAACGACTTTCTTCCTGCTT
genomic: GGACCTTCCTCCTCACCGTTTAGCTGAAATTCGTCGTTTCTTTGAAGATTgtatcctttc ... aaggaattagACAAGAAGAATGAGAACAAGGAAGTTGCAGTGAACGACTTTCTTCCTGCTT
EST: gi|151397331|gb|EV267204.1|EV267204
EST:     GGACCTTCCTCCTCACCGTTTAGCTGAAATTCGTCGTTTCTTTGAAGATT                         ACAAGAAGAATGAGAACAAGGAAGTTGCAGTGAACGACTTTCTTCCTGCTT
genomic: GGACCTTCCTCCTCACCGTTTAGCTGAAATTCGTCGTTTCTTTGAAGATTgtatcctttc ... aaggaattagACAAGAAGAATGAGAACAAGGAAGTTGCAGTGAACGACTTTCTTCCTGCTT
EST: gi|31561493|gb|CD487331.1|CD487331
EST:     GGACCTTCCTCCTCACCGTTTAGCTGAAATTCGTCGTTTCTTTGAAGATT                         ACAAGAAGAATGAGAACAAGGAAGTTGCAGTGAACGACTTTCTTCCTGCTT
genomic: GGACCTTCCTCCTCACCGTTTAGCTGAAATTCGTCGTTTCTTTGAAGATTgtatcctttc ... aaggaattagACAAGAAGAATGAGAACAAGGAAGTTGCAGTGAACGACTTTCTTCCTGCTT
EST: gi|213601035|gb|DB983710.1|DB983710
EST:     CTA-CTTCCTCATAACCGTTTAGCTGAAATACGTCGTTTCTTTGAAGATT                         ACAAGAAGAATGAGAACAAGGAAGTTGCAGTGAACGACTTCCTTCCTGCTT
genomic: -GACCTTCCTCCTCACCGTTTAGCTGAAATTCGTCGTTTCTTTGAAGATTgtatcctttc ... aaggaattagACAAGAAGAATGAGAACAAGGAAGTTGCAGTGAACGACTTTCTTCCTGCTT
EST: gi|58020419|gb|CX707161.1|CX707161
EST:     GGACCTTCCTCCTCACCGTTTAGCTGAAATTCGTCGTTTCTTTGAAGATT                         ACAAGAAGAATGAGAACAAGGAAGTTGCAGTGAACGACTTTCTTCCTGCTT
genomic: GGACCTTCCTCCTCACCGTTTAGCTGAAATTCGTCGTTTCTTTGAAGATTgtatcctttc ... aaggaattagACAAGAAGAATGAGAACAAGGAAGTTGCAGTGAACGACTTTCTTCCTGCTT
EST: gi|22931726|gb|BU548865.1|BU548865
EST:     GGACCTTCCTCCTCACCGTTTAGCTGAAATTCGTCGTTTCTTTGAAGATT                         ACAAGAAGAATGAGAACAAGGAAGTTGCAGTGAACGACTTTCTTCCTGCTT
genomic: GGACCTTCCTCCTCACCGTTTAGCTGAAATTCGTCGTTTCTTTGAAGATTgtatcctttc ... aaggaattagACAAGAAGAATGAGAACAAGGAAGTTGCAGTGAACGACTTTCTTCCTGCTT
EST: gi|192317150|gb|FK009765.1|FK009765
EST:     GGACCTTCCTCCTCACCGTTTAGCTGAAATTCGTCGTTTCTTTGAAGATT                         ACAAGAAGAATGAGAACAAGGAAGTTGCAGTGAACGACTTTCTTCCTGCTT
genomic: GGACCTTCCTCCTCACCGTTTAGCTGAAATTCGTCGTTTCTTTGAAGATTgtatcctttc ... aaggaattagACAAGAAGAATGAGAACAAGGAAGTTGCAGTGAACGACTTTCTTCCTGCTT
EST: gi|192331411|gb|FK022716.1|FK022716
EST:     GGACCTTCCTCCTCACCGTTTAGCTGAAATTCGTCGTTTCTTTGAAGATT                         ACAAGAAGAATGAGAAC
genomic: GGACCTTCCTCCTCACCGTTTAGCTGAAATTCGTCGTTTCTTTGAAGATTgtatcctttc ... aaggaattagACAAGAAGAATGAGAAC
EST: gi|192302348|gb|FG996658.1|FG996658
EST:     GGACCTTCCTCCTCACCGTTTAGCTGAAATTCGTCGTTTCTTTGAAGATT                         ACAAGAAGAATGAGAACAAGGAAGTTGCAGTGAACGACTTTCTTCCTGCTT
genomic: GGACCTTCCTCCTCACCGTTTAGCTGAAATTCGTCGTTTCTTTGAAGATTgtatcctttc ... aaggaattagACAAGAAGAATGAGAACAAGGAAGTTGCAGTGAACGACTTTCTTCCTGCTT
EST: gi|13479092|gb|BG508435.1|BG508435
EST:     GGACCTTCCTCCTCACCGTTTAGCTGAAATTCGTCGTTTCTTTGAAGATT                         ACAAGAAGAATGAGAACAAGGAAGTTGCAGTGAACGACTTTCTTCCTGCTT
genomic: GGACCTTCCTCCTCACCGTTTAGCTGAAATTCGTCGTTTCTTTGAAGATTgtatcctttc ... aaggaattagACAAGAAGAATGAGAACAAGGAAGTTGCAGTGAACGACTTTCTTCCTGCTT
EST: gi|193423930|gb|FK390269.1|FK390269
EST:     GGACCTTCCTCCTCACCGTTTAGCTGAAATTCGTCGTTTCTTTGAAGATT                         ACAAGAAGAATGAGAACAAGGAAGTTGCAGTGAACGACTTTCTTCCTGCTT
genomic: GGACCTTCCTCCTCACCGTTTAGCTGAAATTCGTCGTTTCTTTGAAGATTgtatcctttc ... aaggaattagACAAGAAGAATGAGAACAAGGAAGTTGCAGTGAACGACTTTCTTCCTGCTT
EST: gi|193384347|gb|FK351809.1|FK351809
EST:     GGACCTTCCTCCTCACCGTTTAGCTGAAATTCGTCG-TTCTTTGAAGATT                         ACAAGAAGAATGAGAACAAGGAAGTTGCAGTGAACGACTTTCTTCCTGCTT
genomic: GGACCTTCCTCCTCACCGTTTAGCTGAAATTCGTCGTTTCTTTGAAGATTgtatcctttc ... aaggaattagACAAGAAGAATGAGAACAAGGAAGTTGCAGTGAACGACTTTCTTCCTGCTT
EST: gi|31305438|gb|CD390641.1|CD390641
EST:     GGACCTTCCTCCTCACCGTTTAGCTGAAATTCGTCGTTTCTTTGAAGATT                         ACAAGAAGAATGAGAACAAGGAAGTTGCAGTGAACGACTTTCTTCCTGCTT
genomic: GGACCTTCCTCCTCACCGTTTAGCTGAAATTCGTCGTTTCTTTGAAGATTgtatcctttc ... aaggaattagACAAGAAGAATGAGAACAAGGAAGTTGCAGTGAACGACTTTCTTCCTGCTT
EST: gi|193341625|gb|FK305899.1|FK305899
EST:     GGACCTTCCTCCTCACCGTTTAGCTGAAATTCGTCGTTTCTTTGAAGATT                         ACAAGAAGAATGAGAACAAGGAAGTTGCAGTGAACGACTTTCTTCCTGCTT
genomic: GGACCTTCCTCCTCACCGTTTAGCTGAAATTCGTCGTTTCTTTGAAGATTgtatcctttc ... aaggaattagACAAGAAGAATGAGAACAAGGAAGTTGCAGTGAACGACTTTCTTCCTGCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggcgtgccatataaaatcaaactattttatgttttccttaataaaggaattagACAAGAAGAATGAGAACAAGGAAGTTGCAGTGAACGACTTTCTTCCTGCTTCAGCTGCCTATGAAGCTATCAAGCATTCCAT
 ttccttaat  putative branch site 
          atataaaatcaaacta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatcctttccaagaatttcaaaatgtgtttgttcagtacttcctatatgttagcatctatataggtaatcatttggcgtgccatataaaatcaaactattttatgttttccttaataaaggaattagACAAGAAGAATGAGAACAAGGAAGTTGCAGTGAACGACTTTCTTCCTGCTTCAGCTGCCTATGAAGCTATCAAGCATTCCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC