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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagtttaattgtatgcttttgatggttccattgaccatgataaagctgccatgattagtttgcttgggcatttcatgacaactaaatctttgtcttgtagATCTTCGGGATGATAAGCAGTTCTTTCAAGACCATCCTGGTGCAGTGCCTATCACCACAGCACAG

Basic information

species Glycine max
transcript GLYMA11G11510.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G11510.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os02g02840.1 (Oryza sativa), 3'ss of exon 4
------tagtttaattgta-tgcttttgatggttccattgaccatgataaagctgccatgattagtttgcttgggcatttcatgacaactaaatctttgtcttgtagATCTTCGGGATGATAAGCAGTTCTTTCAAGACCATCCTGGTGCAGTGCCTATCACCACAGCACAG
       | |  |||  |  | |   | ||    || | ||||    ||||| | | |   | ||    |||     |||||       ||    ||   || | ||||||||| ||||| |||||||| |||   |||||||||||||| || ||||||||||| || |||
aaattaaattccaatcattctacagataatatccccttcgacct--gtaaagatccaactgt-agcccacttacatttttcacattgttta----ttgcactggcagATCTTCGAGATGACAAGCAGTTTTTTGTGGACCATCCTGGTGCTGTTCCTATCACCACTGCTCAG

upper sequence: GLYMA11G11510.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM5G803949_T02 (Zea mays), 3'ss of exon 4
tagtttaattgtatg-cttttgatggttccattgaccatgataaagctgcca-tgattagtt-tgcttgggcatttcatgacaactaaatctttgtcttgtagATCTTCGGGATGATAAGCAGTTCTTTCAAGACCATCCTGGTGCAGTGCCTATCACCACAGCACAG
     || | | ||  ||| |       ||   | | |   ||||||  |   |   |||     | |    || || | |||| |  |  |||  ||   ||||||||| ||||| ||||||||||||   |||||||||||||| || |||||||| || || |||
--aactagtggcataacttgtacacaaacccacgcctagagtaaagcctcaggttgctagcagcacatccttatatcttcacaa-tgcacattttactgacagATCTTCGAGATGACAAGCAGTTCTTTGTGGACCATCCTGGTGCTGTTCCTATCACTACTGCTCAG

upper sequence: GLYMA11G11510.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM5G846811_T01 (Zea mays), 3'ss of exon 4
tagtttaattgtatg-cttttgatggttccattgaccatgataaagctgccatgattagtttgcttgggc--atttcatgacaactaaatctttgtcttgtagATCTTCGGGATGATAAGCAGTTCTTTCAAGACCATCCTGGTGCAGTGCCTATCACCACAGCACAG
     || | | |   | | ||   |  ||   |   |  |||||||  |       |   |||     |  || |  | |||| |  |  |||   | | ||||||||| || || ||||||||||||   |||||||||||||| || |||||||| || || |||
--aactagtggcacaacatgtgcgtgaacccacgggtagcataaagcctcaggttgcaagctgcacatccttatattttcacaa-tgcacatttcattggcagATCTTCGAGACGACAAGCAGTTCTTTGTGGACCATCCTGGTGCTGTCCCTATCACTACTGCTCAG

upper sequence: GLYMA11G11510.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv03s0038g02380.t01 (Vitis vinifera), 3'ss of exon 5
tagtttaattgtatgcttttgatggttccattgaccatgataaagctgccatgattagtttgcttgggcatttcatgacaactaaatct---ttgtcttgtagATCTTCGGGATGATAAGCAGTTCTTTCAAGACCATCCTGGTGCAGTGCCTATCACCACAGCACAG
 || |   || | || ||   ||  ||| |   || || |    | | || |      |||      || ||  |||  || ||  |     ||  |||||||||||||| |||||||||||||||||   ||| || |||||||||||||| || |||||||| |||
gagatgctttttgtgtttacaata-ttctag-aactataaatgtgat-ccctttcccttttcaacaagccttcaatgctaattacttgcaaatttgcttgtagATCTTCGAGATGATAAGCAGTTCTTCATAGATCACCCTGGTGCAGTGCCCATTACCACAGCTCAG

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|7589435|gb|AW705209.1|AW705209
EST:     GAGGCATTATGCTCCTGGTGTTCCAATTATTCTTGTTGGAACAAAACTTG                         ATCTTCGGGATGATAAGCAGTTCTTTCAAGACCATCCTGGTGCAGTGCCTA
genomic: GAGGCATTATGCTCCTGGTGTTCCAATTATTCTTGTTGGAACAAAACTTGgtcagattct ... tgtcttgtagATCTTCGGGATGATAAGCAGTTCTTTCAAGACCATCCTGGTGCAGTGCCTA
EST: gi|298169211|gb|HO020571.1|HO020571
EST:     GAGGCATTATGCTCCTGGTGTTCCAATTATTCTTGTTGGAACAAAACTTG                         ATCTTCGGGATGATAAGCAGTTCTTTCAAGACCATCCTGGTGCAGTGCCTA
genomic: GAGGCATTATGCTCCTGGTGTTCCAATTATTCTTGTTGGAACAAAACTTGgtcagattct ... tgtcttgtagATCTTCGGGATGATAAGCAGTTCTTTCAAGACCATCCTGGTGCAGTGCCTA
EST: gi|298197330|gb|HO044809.1|HO044809
EST:     GAGGCATTATGCTCCTGGTGTTCCAATTATTCTTGTTGGAACAAAACTTG                         ATCTTCGGGATGATAAGCAGTTCTTTCAAGACCATCCTGGTGCAGTGCCTA
genomic: GAGGCATTATGCTCCTGGTGTTCCAATTATTCTTGTTGGAACAAAACTTGgtcagattct ... tgtcttgtagATCTTCGGGATGATAAGCAGTTCTTTCAAGACCATCCTGGTGCAGTGCCTA
EST: gi|298171990|gb|HO021582.1|HO021582
EST:     GAGGCATTATGCTCCTGGTGTTCCAATTATTCTTGTTGGAACAAAACTTG                         ATCTTCGGGATGATAAGCAGTTCTTTCAAGACCATCCTGGTGCAGTGCCTA
genomic: GAGGCATTATGCTCCTGGTGTTCCAATTATTCTTGTTGGAACAAAACTTGgtcagattct ... tgtcttgtagATCTTCGGGATGATAAGCAGTTCTTTCAAGACCATCCTGGTGCAGTGCCTA
EST: gi|16996922|gb|BM086294.1|BM086294
EST:     GAGGCATTATGCTCCTGGTGTTCCAATTATTCTTGTTGGAACAAAACTTG                         ATCTTCGGGATGATAAGCAGTTCTTTCAAGACCATCCTGGTGCAGTGCCTA
genomic: GAGGCATTATGCTCCTGGTGTTCCAATTATTCTTGTTGGAACAAAACTTGgtcagattct ... tgtcttgtagATCTTCGGGATGATAAGCAGTTCTTTCAAGACCATCCTGGTGCAGTGCCTA
EST: gi|193681399|gb|FK623261.1|FK623261
EST:     AGGCATTATGCTCCTGGTGTTTCCAATTATTCTTGTTGGAACAAAACTTG                         ATCTTCGGGATGATAAGCAGTTCTTTCAAGACCATCCTGGTGCAGTGCCTA
genomic: AGGCATTATGCTCCTGGTG-TTCCAATTATTCTTGTTGGAACAAAACTTGgtcagattct ... tgtcttgtagATCTTCGGGATGATAAGCAGTTCTTTCAAGACCATCCTGGTGCAGTGCCTA
EST: gi|5760314|gb|AI965741.1|AI965741
EST:     GAGGCATTATGCTCCTGGTGTTCCAATTATTCTTGTTGGAACAAAACTTG                         ATCTTCGGGATGATAAGCAGTTCTTTCAAGACCATCCTGGTGCAGTGCCTA
genomic: GAGGCATTATGCTCCTGGTGTTCCAATTATTCTTGTTGGAACAAAACTTGgtcagattct ... tgtcttgtagATCTTCGGGATGATAAGCAGTTCTTTCAAGACCATCCTGGTGCAGTGCCTA
EST: gi|151394170|gb|EV264041.1|EV264041
EST:     GAGGCATTATGCTCCTGGTGTTCCAATTATTCTTGTTGGAACAAAACTTG                         ATCTTCGGGATGATAAGCAGTTCTTTCAAGACCATCCTGGTGCAGTGCCTA
genomic: GAGGCATTATGCTCCTGGTGTTCCAATTATTCTTGTTGGAACAAAACTTGgtcagattct ... tgtcttgtagATCTTCGGGATGATAAGCAGTTCTTTCAAGACCATCCTGGTGCAGTGCCTA
EST: gi|19346953|gb|BM891833.1|BM891833
EST:     GAGGCATTATGCTCCTGGTGTTCCAATTATTCTTGTTGGAACAAAACTTG                         ATCTTCGGGATGATAAGCAGTTCTTTCAAGACCATCCTGGTGCAGTGCCTA
genomic: GAGGCATTATGCTCCTGGTGTTCCAATTATTCTTGTTGGAACAAAACTTGgtcagattct ... tgtcttgtagATCTTCGGGATGATAAGCAGTTCTTTCAAGACCATCCTGGTGCAGTGCCTA
EST: gi|298177328|gb|HO027109.1|HO027109
EST:     GAGGCATTATGCTCCTGGTGTTCCAATTATTCTTGTTGGAACAAAACTTG                         ATCTTCGGGATGATAAGCAGTTCTTTCAAGACCATCCTGGTGCAGTGCCTA
genomic: GAGGCATTATGCTCCTGGTGTTCCAATTATTCTTGTTGGAACAAAACTTGgtcagattct ... tgtcttgtagATCTTCGGGATGATAAGCAGTTCTTTCAAGACCATCCTGGTGCAGTGCCTA
EST: gi|193599687|gb|FK551538.1|FK551538
EST:     GAGGCATTATGCTCCTGGTGTTCCAATTATTCTTGTTGGAACAAAACTTG                         ATCTTCGGGATGATAAGCAGTTCTTTCAAGACCATCCTGGTGCAGTGCCTA
genomic: GAGGCATTATGCTCCTGGTGTTCCAATTATTCTTGTTGGAACAAAACTTGgtcagattct ... tgtcttgtagATCTTCGGGATGATAAGCAGTTCTTTCAAGACCATCCTGGTGCAGTGCCTA
EST: gi|26058249|gb|CA801163.1|CA801163
EST:     GAGGCATTATGCTCCTGGTGTTCCAATTATTCTTGTTGGAACAAAACTTG                         ATCTTCGGGATGATAAGCAGTTCTTTCAAGACCATCCTGGTGCAGTGCCTA
genomic: GAGGCATTATGCTCCTGGTGTTCCAATTATTCTTGTTGGAACAAAACTTGgtcagattct ... tgtcttgtagATCTTCGGGATGATAAGCAGTTCTTTCAAGACCATCCTGGTGCAGTGCCTA
EST: gi|5342846|gb|AI795130.1|AI795130
EST:     GAGGCATTATGCTCCTGGAGTTCCAATTATTCTTGTTGGAACAAAACTTG                         ATCTTCGGGATGATAAGCAGTTCTTTCAAGACCAT
genomic: GAGGCATTATGCTCCTGGTGTTCCAATTATTCTTGTTGGAACAAAACTTGgtcagattct ... tgtcttgtagATCTTCGGGATGATAAGCAGTTCTTTCAAGACCAT
EST: gi|298182534|gb|HO031269.1|HO031269
EST:     GGGGCATTATGCTCCTGGTGTTCCAATTATTCTTGTTGGAACAAAACTTG                         ATCTTCGGGATGATAAGCAGTTCTTTCAAGACCATCCTGGTGCAGTGCCTA
genomic: GAGGCATTATGCTCCTGGTGTTCCAATTATTCTTGTTGGAACAAAACTTGgtcagattct ... tgtcttgtagATCTTCGGGATGATAAGCAGTTCTTTCAAGACCATCCTGGTGCAGTGCCTA
EST: gi|193642127|gb|FK589733.1|FK589733
EST:     AACAAAACTTG                         ATCTTCGGGATGATAAGCAGTTCTTTCAAGACCATCCTGGTGCAGTGCCTA
genomic: AACAAAACTTGgtcagattct ... tgtcttgtagATCTTCGGGATGATAAGCAGTTCTTTCAAGACCATCCTGGTGCAGTGCCTA
EST: gi|298178107|gb|HO027490.1|HO027490
EST:     GAGGCATTATGCTCCTGGTGTTCCAATTATTCTTGTTGGAACAAAACTTG                         ATCTTCGGGATGATAAGCAGTTCTTTCAAGACCATCCTGGTGCAGTGCCTA
genomic: GAGGCATTATGCTCCTGGTGTTCCAATTATTCTTGTTGGAACAAAACTTGgtcagattct ... tgtcttgtagATCTTCGGGATGATAAGCAGTTCTTTCAAGACCATCCTGGTGCAGTGCCTA
EST: gi|193350327|gb|FK315329.1|FK315329
EST:     GAGGCATTATGCTCCTGGTGTTCCAATTATTCTTGTTGGAACAAAACTTG                         ATCTTCGGGATGATAAGCAGTTCTTTCAAGACCATCCTGGTGCAGTGCCTA
genomic: GAGGCATTATGCTCCTGGTGTTCCAATTATTCTTGTTGGAACAAAACTTGgtcagattct ... tgtcttgtagATCTTCGGGATGATAAGCAGTTCTTTCAAGACCATCCTGGTGCAGTGCCTA
EST: gi|4293505|gb|AI442057.1|AI442057
EST:     GAGGCATTATGCTCCTGGTGTTCCAATTATTCTTGTTGGAACAAAACTTG                         ATCTTCGGGATGATAAGCAGTTCTTTCAAGACCATTCTGGTGCAGTGCCTA
genomic: GAGGCATTATGCTCCTGGTGTTCCAATTATTCTTGTTGGAACAAAACTTGgtcagattct ... tgtcttgtagATCTTCGGGATGATAAGCAGTTCTTTCAAGACCATCCTGGTGCAGTGCCTA
EST: gi|192329017|gb|FK021091.1|FK021091
EST:     GAGGCATTATGCTCCCGGTGTTCCAATTATTCTTGTTGGAACAAAACTTG                         ATCTTCGGGATGATAAGCAGTTCTTTCAAGACCATCCTGGTGCAGTGCCTA
genomic: GAGGCATTATGCTCCTGGTGTTCCAATTATTCTTGTTGGAACAAAACTTGgtcagattct ... tgtcttgtagATCTTCGGGATGATAAGCAGTTCTTTCAAGACCATCCTGGTGCAGTGCCTA
EST: gi|192297529|gb|FG989535.1|FG989535
EST:     GAGGCATTATGCTCCTGGTGTTCCAATTATTCTTGTTGGAACAAAACTTG                         ATCTTCGGGATGATAAGCAGTTCTTTCAAGACCATCCTGGTGCAGTGCCTA
genomic: GAGGCATTATGCTCCTGGTGTTCCAATTATTCTTGTTGGAACAAAACTTGgtcagattct ... tgtcttgtagATCTTCGGGATGATAAGCAGTTCTTTCAAGACCATCCTGGTGCAGTGCCTA
EST: gi|7589250|gb|AW705028.1|AW705028
EST:     GAGGCATTATGCTCCTGGTGTTCCAATTATTCTTGTTGGAACAAAACTTG                         ATCTTCNGGATGATAAGCAGTTCTTTCAAGACCATCCTGGTGCAGTGCCTA
genomic: GAGGCATTATGCTCCTGGTGTTCCAATTATTCTTGTTGGAACAAAACTTGgtcagattct ... tgtcttgtagATCTTCGGGATGATAAGCAGTTCTTTCAAGACCATCCTGGTGCAGTGCCTA
EST: gi|192329018|gb|FK021092.1|FK021092
EST:     GAGGCATTATGCTCCCGGTGTTCCAATTATTCTTGTTGGAACAAAACTTG                         ATCTTCGGGATGATAAGCAGTTCTTTCAAGACCATCCTGGTGCAGTGCCTA
genomic: GAGGCATTATGCTCCTGGTGTTCCAATTATTCTTGTTGGAACAAAACTTGgtcagattct ... tgtcttgtagATCTTCGGGATGATAAGCAGTTCTTTCAAGACCATCCTGGTGCAGTGCCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgccatgattagtttgcttgggcatttcatgacaactaaatctttgtcttgtagATCTTCGGGATGATAAGCAGTTCTTTCAAGACCATCCTGGTGCAGTGCCTATCACCACAGCACAG
                                  aactaaa  putative branch site (score: 2)
                                         tctttgtctt  CT-rich tract
                                     taaatcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagtttaattgtatgcttttgatggttccattgaccatgataaagctgccatgattagtttgcttgggcatttcatgacaactaaatctttgtcttgtagATCTTCGGGATGATAAGCAGTTCTTTCAAGACCATCCTGGTGCAGTGCCTATCACCACAGCACAG

- - - - - gtatgct
- - - - - - - - - - - tggttcc
- - - - - - - - - - - - - - - - - ccatgat
- - - - - - - - - - - - - - - - - - - - - aagctgc
- - - - - - - - - - - - - - - - - - - - - - - - -catgatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcatgac