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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gattgactcattgatgtatcatccttgtgcttgcaatggcatttcttcattttttcttcttatttttacttatgctgcaacattgatttgtgtgtgacagTGAGACAGTGAAATTTGGCCATGTCACATTTTTCTGGAATGGTAACCGCTCGGGATACTTTGATGAAACTAAGGAAGAGTATGTAGAAGTTCCTAGTGAC

Basic information

species Zea mays
transcript GRMZM2G003385_T02
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G003385_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os01g60190.1 (Oryza sativa), 3'ss of exon 6
gattgactcattgatgtatcatccttgtgcttgcaatggcatttcttcattttttcttcttatttttacttatgctgcaac--attgatttgtgtgtg-acagTGAGACAGTGAAATTTGGCCATGTCACATTTTTCTGGAATGGTAACCGCTCGGGATACTTTGATGAAACTAAGGAAGAGTATGTAGAAGTTCCTAGTGAC
 ||||     || ||   |     ||||||||  | |   ||    |  | | ||  ||  |||| || |||||||| |||  |||||||||| | |  |||||||||||||||| |||||||||||||||||||||||||| || ||||| || ||||||||||||||||||||||||||||| || ||| |||||||||| 
-attgtggagtttatagttgtctattgtgcttata-taaaataatattctgtcttagtcc-atttgtatttatgctgtaactcattgatttgtttttttacagTGAGACAGTGAAGTTTGGCCATGTCACATTTTTCTGGAACGGAAACCGATCTGGATACTTTGATGAAACTAAGGAAGAGTACGTTGAAATTCCTAGTGAT

upper sequence: GRMZM2G003385_T02 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA09G40690.1 (Glycine max), 3'ss of exon 5
gattgactcattgatgtatcatccttgtgcttgcaatggcatttcttcattttttcttcttatttttacttatg-ctgcaacattgatttgtgtg-----------tgacagTGAGACAGTGAAATTTGGCCATGTCACATTTTTCTGGAATGGTAACCGCTCGGGATACTTTGATGAAACTAAGGAAGAGTATGTAGAAGTTCCTAGTGAC
              || | |||  |  |      ||   |  ||| | || |  |  |  | | || | | ||| |    | | | | |||| ||             |||||||||| || |||||||| || |||||||| ||||||||||| |||||||| || || ||| ||  |     ||| |||||||| ||| |||| ||||||
------------tttgcaacattttgtttaccttaagaactcttcattatctagtacttatctgttaaatgatggccatcatagtcacttgtatgaatttctttgtcaacagTGAGACTGTTAAATTTGGTCACGTCACATTCTTCTGGAATGGAAACCGCTCTGGGTATTTTAATTCAGAATTGGAGGAGTATGTGGAAATTCCCAGTGAC

upper sequence: GRMZM2G003385_T02 (Zea mays), 3'ss of exon 6
lower sequence: AT3G08590.2 (Arabidopsis thaliana), 3'ss of exon 4
--gattgactcattgatgt-atcatccttgtgcttgc-aatggcatttcttcattttttcttcttatttttacttatgctgcaacattgatttgtgtgtgacagTGAGACAGTGAAATTTGGCCATGTCACATTTTTCTGGAATGGTAACCGCTCGGGATACTTTGATGAAACTAAGGAAGAGTATGTAGAAGTTCCTAGTGAC
   | |   || ||||||  || || |   || | |  | |  ||| |  | | |   |  ||   | || || |||  |  ||  || ||||   ||  |||||||||| ||||| ||||||||||| || || ||||||||||| |||||||| ||||| ||  ||||||     |||||||| || ||  |||| ||||| 
ctcactttttc-ttgatgagattataccgttgatggttagttacatataatgaatgaattctcagctattaacctat--taaaatttt-atttcactgaaacagTGAGACTGTGAAGTTTGGCCATGTAACCTTCTTCTGGAATGGCAACCGCTCTGGATATTTCAATGAAAAGTTAGAAGAGTACGTTGAGATTCCAAGTGAT

upper sequence: GRMZM2G003385_T02 (Zea mays), 3'ss of exon 6
lower sequence: Vv08s0056g00200.t01 (Vitis vinifera), 3'ss of exon 5
gattgactcattgatgtatcatccttgtgcttgcaatggcatttcttcattttttcttcttatttttacttatgctgcaacattgatttgtgtgtgacagTGAGACAGTGAAATTTGGCCATGTCACATTTTTCTGGAATGGTAACCGCTCGGGATACTTTGATGAAACTAAGGAAGAGTATGTAGAAGTTCCTAGTGAC
||  |  |  || |||  |  |  | |    |       || |||  || |||||  |   ||| |    | |    |    ||  | | | | | |||||||||| || |||||||| ||||| || |||||||||||||| || ||||| || || ||||||  || || ||| || ||||||||| |||| ||||| 
gagggtttatttcatggttagtgataggttctttttcttcaattcaccagtttttaataccattctctgctgtctaactctctttttctttctttaacagTGAGACTGTCAAATTTGGTCATGTTACCTTTTTCTGGAATGGAAATCGCTCAGGGTATTTTGATCCAAGTATGGAGGAATATGTAGAAATTCCCAGTGAT

upper sequence: GRMZM2G003385_T02 (Zea mays), 3'ss of exon 6
lower sequence: PP1S145_164V6.2 (Physcomitrella patens), 3'ss of exon 6
-------------------------------------------------gattgactc--attgatgtatcatccttgtgcttgcaatggcatttcttcattttttcttcttatttttacttatgctgcaacattgatttgtgtgtgacagTGAGACAGTGAAATTTGGCCATGTCACATTTTTCTGGAATGGTAACCGCTCGGGATACTTTGATGAAACTAAGGAAGAGTATGTAGAAGTTCCTAGTGAC
                                                   |  |||   | |    | | |   || |  ||| || | || ||    | |   |  | |    | |||   | ||  | || | | ||| || || |||||| || || ||||| |||||||| |||||| ||||||||||||| ||||| ||  | |||   || ||    ||| | || ||  || ||||||| || 
gtaaggagtattccacatcatagaccacactgtctgcgcgttaggagcaagtaaacttcaaattccttgttaggattctttttgtaaagacagttgcgtagtgggtagtttacagtctaca-gttcta-atcaataaattgggt-tggcagTGAAACGGTCAAATTCGGCCATGTGACATTTGTCTGGAATGGTAATCGCTCTGGCCAGTTTAGCGATACCCTTGAAAAATACGTTCAAATTCCTAGCGAT

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|116818022|gb|EC860953.1|EC860953
EST:     ACATCTGGGGAGTACTTGGTGAAGAATGGCATCCGCACCTTTGCTTGCAG                         TGAGACAGTGAAATTTGGCCATGTCACATTTTTCTGGAACGGTAACCGCTC
genomic: ACATCTGGGGAGTACTTGGTGAAGAATGGCATCCGCACCTTTGCTTGCAGgcaagtacta ... tgtgtgacagTGAGACAGTGAAATTTGGCCATGTCACATTTTTCTGGAATGGTAACCGCTC
EST: gi|60345366|gb|DN212339.1|DN212339
EST:     ACATCTGGGGAGTACTTGGTGAAGAATGGCATCCGCACCTTTGCTTGCAG                         TGAGACAGTGAAATTTGGCCATGTCACATTTTTCTGGAACGGCAACCGCTC
genomic: ACATCTGGGGAGTACTTGGTGAAGAATGGCATCCGCACCTTTGCTTGCAGgcaagtacta ... tgtgtgacagTGAGACAGTGAAATTTGGCCATGTCACATTTTTCTGGAATGGTAACCGCTC
EST: gi|67024990|gb|CO453739.1|CO453739
EST:     ACATCTGGGGAGTACTTGGTGAAGAATGGCATCCGCACCTTTGCTTGCAG                         TGAGACAGTGAAATTTGGCCATGTCACATTTTTCTGGAACGGTAACCGCTC
genomic: ACATCTGGGGAGTACTTGGTGAAGAATGGCATCCGCACCTTTGCTTGCAGgcaagtacta ... tgtgtgacagTGAGACAGTGAAATTTGGCCATGTCACATTTTTCTGGAATGGTAACCGCTC
EST: gi|67018390|gb|CO447139.1|CO447139
EST:     ACATCTGGGGAGTACTTGGTGAAGAATGGCATCCGCACCTTTGCTTGCAG                         TGAGACAGTGAAATTTGGCCATGTCACATTTTTCTGGAACGGTAACCGCTC
genomic: ACATCTGGGGAGTACTTGGTGAAGAATGGCATCCGCACCTTTGCTTGCAGgcaagtacta ... tgtgtgacagTGAGACAGTGAAATTTGGCCATGTCACATTTTTCTGGAATGGTAACCGCTC
EST: gi|213192767|gb|FM182154.1|FM182154
EST:     ACATCTGGGGAGTACTTGGTGAAGAATGGCATCCGCACCTTTGCTTGCAG                         TGAGACAGTGAAATTTGGCCATGTCGCATTTTTCTGGAATGGTAACCGCTC
genomic: ACATCTGGGGAGTACTTGGTGAAGAATGGCATCCGCACCTTTGCTTGCAGgcaagtacta ... tgtgtgacagTGAGACAGTGAAATTTGGCCATGTCACATTTTTCTGGAATGGTAACCGCTC
EST: gi|6564102|gb|AW231724.1|AW231724
EST:     ACATCTGGGGAGTACTTGGTGAAGAATGGCATCCGCACCTTTGCTTGCAG                         TGAGACAGTGAAATTTGGCCATGTCACATTTTTCTGGAACGGCAACCGCTC
genomic: ACATCTGGGGAGTACTTGGTGAAGAATGGCATCCGCACCTTTGCTTGCAGgcaagtacta ... tgtgtgacagTGAGACAGTGAAATTTGGCCATGTCACATTTTTCTGGAATGGTAACCGCTC
EST: gi|31361690|gb|CD446047.1|CD446047
EST:     ACATCTGGGGAGTACTTGGTGAAGAATGGCATCCGCACCTTTGCTTGCAG                         TGAGACAGTGAAATTTGGCCATGTCACATTTTTCTGGAACGGTAACCGCTC
genomic: ACATCTGGGGAGTACTTGGTGAAGAATGGCATCCGCACCTTTGCTTGCAGgcaagtacta ... tgtgtgacagTGAGACAGTGAAATTTGGCCATGTCACATTTTTCTGGAATGGTAACCGCTC
EST: gi|7262366|gb|AW585309.1|AW585309
EST:     ACATCTGGGGAGTACTTGGTGAAGAATGGCATCCGCACCTTTGCTTGCAG                         TGAGACAGTGAAATTTGGCCATGTCACATTT
genomic: ACATCTGGGGAGTACTTGGTGAAGAATGGCATCCGCACCTTTGCTTGCAGgcaagtacta ... tgtgtgacagTGAGACAGTGAAATTTGGCCATGTCACATTT
EST: gi|211242235|gb|FL127855.1|FL127855
EST:     ACATCTGGGGAGTACTTGGTGAAGAATGGCATCCGCACCTTTGCTTGCAG                         TGAGACAGTGAAATTTGGCCATGTCACATTTTTCTGGAATGGTAACCGCTC
genomic: ACATCTGGGGAGTACTTGGTGAAGAATGGCATCCGCACCTTTGCTTGCAGgcaagtacta ... tgtgtgacagTGAGACAGTGAAATTTGGCCATGTCACATTTTTCTGGAATGGTAACCGCTC
EST: gi|31354846|gb|CD439203.1|CD439203
EST:     ACATCTGGGGAGTACTTGGTGAAGAATGGCATCCGCACCTTTGCTTGCAG                         TGAGACAGTGAAATTTGGCCATGTCACATTTTTCTGGAACGGTAACCGCTC
genomic: ACATCTGGGGAGTACTTGGTGAAGAATGGCATCCGCACCTTTGCTTGCAGgcaagtacta ... tgtgtgacagTGAGACAGTGAAATTTGGCCATGTCACATTTTTCTGGAATGGTAACCGCTC
EST: gi|32844262|gb|CD983943.1|CD983943
EST:     ACTTGGTGAAGAATGGCATCCGCACCTTTGCTTGCAG                         TGAGACAGTGAAATTTGGCCATGTCACATTTTTCTGGAATGGTAACCGCTC
genomic: ACTTGGTGAAGAATGGCATCCGCACCTTTGCTTGCAGgcaagtacta ... tgtgtgacagTGAGACAGTGAAATTTGGCCATGTCACATTTTTCTGGAATGGTAACCGCTC
EST: gi|211240011|gb|FL127851.1|FL127851
EST:     ACATCTGGGGAGTACTTGGTGAAGAATGGCATCCGCACCTTTGCTTGCAG                         TGAGACAGTGAAATTTGGCCATGTCACATTTTTCTGGAACGGTAACCGCTC
genomic: ACATCTGGGGAGTACTTGGTGAAGAATGGCATCCGCACCTTTGCTTGCAGgcaagtacta ... tgtgtgacagTGAGACAGTGAAATTTGGCCATGTCACATTTTTCTGGAATGGTAACCGCTC
EST: gi|32850328|gb|CD990009.1|CD990009
EST:     ACTTGGTGAAGAATGGCATCCGCACCTTTGCTTGCAG                         TGAGACAGTGAAATTTGGCCATGTCACATTTTTCTGGAATGGTAACCGCTC
genomic: ACTTGGTGAAGAATGGCATCCGCACCTTTGCTTGCAGgcaagtacta ... tgtgtgacagTGAGACAGTGAAATTTGGCCATGTCACATTTTTCTGGAATGGTAACCGCTC
EST: gi|40336839|gb|CK370909.1|CK370909
EST:     ACATCTGGGGAGTACTTGGTGAAGAATGGCATCCGCACCTTTGCTTGCAG                         TGAGACAGTGAAATTTGGCCATGTCACATTTTTCTGGAATGGTAACCGCTC
genomic: ACATCTGGGGAGTACTTGGTGAAGAATGGCATCCGCACCTTTGCTTGCAGgcaagtacta ... tgtgtgacagTGAGACAGTGAAATTTGGCCATGTCACATTTTTCTGGAATGGTAACCGCTC
EST: gi|116820113|gb|EC863305.1|EC863305
EST:     ACATCTGGGGAGTACTTGGTGAAGAATGGCATCCGCACCTTTGCTTGCAG                         TGAGACAGTGAAATTTGGCCATGTCACATTTTTCTGGAACGGTAACCGCTC
genomic: ACATCTGGGGAGTACTTGGTGAAGAATGGCATCCGCACCTTTGCTTGCAGgcaagtacta ... tgtgtgacagTGAGACAGTGAAATTTGGCCATGTCACATTTTTCTGGAATGGTAACCGCTC
EST: gi|32844863|gb|CD984544.1|CD984544
EST:     ACTTGGTGAAGAATGGCATCCGCACCTTTGCTTGCAG                         TGAGACAGTGAAATTTGGCCATGTCACATTTTTCTGGAATGGTAACCGCTC
genomic: ACTTGGTGAAGAATGGCATCCGCACCTTTGCTTGCAGgcaagtacta ... tgtgtgacagTGAGACAGTGAAATTTGGCCATGTCACATTTTTCTGGAATGGTAACCGCTC
EST: gi|6973420|gb|AW438114.1|AW438114
EST:     ACATCTGCGGAGTACTTGGTGAAGAATGGCATCCGCACCTTTGCTTGCAG                         TGAGACAGTGAAATTTGGCCATGTCACATTTTTCTGGAATGGTAACCGCTC
genomic: ACATCTGGGGAGTACTTGGTGAAGAATGGCATCCGCACCTTTGCTTGCAGgcaagtacta ... tgtgtgacagTGAGACAGTGAAATTTGGCCATGTCACATTTTTCTGGAATGGTAACCGCTC

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 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 311

AGTTGAAGCTTCCAAGTCGCTACCTTGTTTCCCCACCAGAGATAGATAGAACATCTGGGGAGTACTTGGTGAAGAATGGCATCCGCACCTTTGCTTGCAGgcaagtacta ... tgtgtgacagTGAGACAGTGAAATTTGGCCATGTCACATTTTTCTGGAATGGTAACCGCTCGGGATACTTTGATGAAACTAAGGAAGAGTATGTAGAAGTTCCTAGTGAC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 512

AGTTGAAGCTTCCAAGTCGCTACCTTGTTTCCCCACCAGAGATAGATAGAACATCTGGGGAGTACTTGGTGAAGAATGGCATCCGCACCTTTGCTTGCAGgcaagtacta ... tgtgtgacagTGAGACAGTGAAATTTGGCCATGTCACATTTTTCTGGAATGGTAACCGCTCGGGATACTTTGATGAAACTAAGGAAGAGTATGTAGAAGTTCCTAGTGAC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 377

AGTTGAAGCTTCCAAGTCGCTACCTTGTTTCCCCACCAGAGATAGATAGAACATCTGGGGAGTACTTGGTGAAGAATGGCATCCGCACCTTTGCTTGCAGgcaagtacta ... tgtgtgacagTGAGACAGTGAAATTTGGCCATGTCACATTTTTCTGGAATGGTAACCGCTCGGGATACTTTGATGAAACTAAGGAAGAGTATGTAGAAGTTCCTAGTGAC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 684

AGTTGAAGCTTCCAAGTCGCTACCTTGTTTCCCCACCAGAGATAGATAGAACATCTGGGGAGTACTTGGTGAAGAATGGCATCCGCACCTTTGCTTGCAGgcaagtacta ... tgtgtgacagTGAGACAGTGAAATTTGGCCATGTCACATTTTTCTGGAATGGTAACCGCTCGGGATACTTTGATGAAACTAAGGAAGAGTATGTAGAAGTTCCTAGTGAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcattttttcttcttatttttacttatgctgcaacattgatttgtgtgtgacagTGAGACAGTGAAATTTGGCCATGTCACATTTTTCTGGAATGGTAACCGCTCGGGATACTTTGATGAAACTAAGGAAGAGTATGTAGAAGTTCCTAGTGAC
                                   cattgat  putative branch site (score: 684)
     tttttcttcttatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gattgactcattgatgtatcatccttgtgcttgcaatggcatttcttcattttttcttcttatttttacttatgctgcaacattgatttgtgtgtgacagTGAGACAGTGAAATTTGGCCATGTCACATTTTTCTGGAATGGTAACCGCTCGGGATACTTTGATGAAACTAAGGAAGAGTATGTAGAAGTTCCTAGTGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - -tgatgta
- - - - - - - - - - - - - -tgcttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatttg