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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagcatttgacatctatttattttgaagaacttttcattgtttcatctatttcgtacttgtcaatattgaatttatttctcctttgtttgtttagATCCTGTTTGTTATATCAAAACCAGATGTTTTCAAGAGCCCGACTTCTGACACATACATTATATTCGGCGAAGCCAAGATTGAAGACTTGAGCTCACAGC

Basic information

species Glycine max
transcript GLYMA03G27580.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G27580.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G465333_T01 (Zea mays), 3'ss of exon 3
---------gttagcatttgacatctatttattttgaagaacttttcattgt-ttcatctatttcgtacttgtcaatattgaatt-tatttctcctttgtttgtttagATCCTGTTTGTTATATCAAAACCAGATGTTTTCAAGAGCCCGACTTCTGACACATACATTATATTCGGCGAAGCCAAGATTGAAGACTTGAGCTCACAGC
               |  || | | | |||||| |        |  ||| || |  ||    ||  |  |||||    |   ||  ||  |   | |  |||    |||| |||||||| || || || |||||||| |||||||||||||  || ||||||||| | ||||||||||| |||||||| || ||| | ||||| ||||
gtaattcaccacgcaaactggcctatctttattgttgtctggctaacatggtatatattatctttattgttgtctggctaacatgataaatgcacatatttttcccagATACTGTTTGTCATCTCGAAGCCAGATGTGTTCAAGAGCCCGAACTCAGACACATACGTCATATTCGGCGAGGCCAAGATCGAGGACCTCAGCTCCCAGC

upper sequence: GLYMA03G27580.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G000923_T01 (Zea mays), 3'ss of exon 3
gttagcatttgacatctatttattttgaagaacttttcattgtttcatctatttcgtacttgtcaatattgaatttatttctcctttgtttgtttagATCCTGTTTGTTATATCAAAACCAGATGTTTTCAAGAGCCCGACTTCTGACACATACATTATATTCGGCGAAGCCAAGATTGAAGACTTGAGCTCACAGC
      |||   ||| || | |  |   | ||  |  | |   || || | || |   || |  || ||   || |  |  | |           |||| || ||||| || || ||||||||||| ||||||||||||| ||| ||||| ||  | ||||||||||| || ||||| || ||| | ||||| ||||
---gtaattcaccatttactcagatcacacaaactggcttatctttat-tgttgc---ctggctaacat--gatatgctatttcc----------agATACTCTTTGTCATCTCCAAACCAGATGTGTTCAAGAGCCCGAATTCCGACACGTATGTCATATTCGGCGAGGCTAAGATCGAGGACCTCAGCTCCCAGC

upper sequence: GLYMA03G27580.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv13s0067g00710.t01 (Vitis vinifera), 3'ss of exon 3
--------------------------------------gttagcatttgacatctatttattttgaagaacttttcattgtttcatctatttcgtacttgtcaatattgaatttatttctcctttgtttgtttagATCCTGTTTGTTATATCAAAACCAGATGTTTTCAAGAGCCCGACTTCTGACACATACATTATATTCGGCGAAGCCAAGATTGAAGACTTGAGCTCACAGC
                                        | ||     |   |   |    || |     || || |  |||  ||       |     ||  |  | |  |   || |   ||| |   | ||||| ||||||| ||||||||||||||||| ||||||||||| || || || |||||  | || || ||||| || |||||||||||||||||||||||||
gttagtttccctctcttttctttgtgtgtatattcccctcttgctccccatgccccatctgcttaatccttttgtcctccttttgtcctccctttgaacttctgttgtaatctcggttattacttgcta--tcagATCTTGTTTGTCATATCAAAACCAGATGTCTTCAAGAGCCCAACATCAGATACATATGTCATTTTTGGCGAGGCAAAGATTGAAGACTTGAGCTCACAGC

upper sequence: GLYMA03G27580.2 (Glycine max), 3'ss of exon 3
lower sequence: PP1S10_319V6.1 (Physcomitrella patens), 3'ss of exon 3
gttagcatttgacatctatttattttgaagaacttttcattgtttcatctatttc--gtacttgtcaatattgaatttatttctcctttgtttgttt---agATCCTGTTTGTTATATCAAAACCAGATGTTTTCAAGAGCCCGACTTCTGACACATACATTATATTCGGCGAAGCCAAGATTGAAGACTTGAGCTCACAGC
   |  || |   | || | | |||    |  ||| ||  ||| |  ||| |     | | |      | |||  ||     |    ||||    ||   ||||||| || || || ||    || ||||| |||||||||||  | || ||||| |||||||| || ||||||||||||||||| |||||||| || || |
--aaatatctccgaactgtatttttcagtgtgcttatctgtgtctggtctctgaaaagcaatgtattctgttggcttacgaccaatgttgtaaaatttgcagATCCTCTTCGTGATCTCCGCTCCTGATGTGTTCAAGAGCCCTGCATCAGACACGTACATTATCTTTGGCGAAGCCAAGATTGAGGACTTGAGTTCTCAAC

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|151412287|gb|EV282099.1|EV282099
EST:     TGAAGCCTGTCACAGGTGTCAGTCGTGTGACTGTTAAGAAGAGCAAAAAT                         ATCCTGTTTGTTATATCAAAACCAGATGTTTTCAAGAGCCCCGACTTCTGA
genomic: TGAAACCTGTCACAGGTGTCAGTCGTGTGACTGTTAAGAAGAGCAAAAATgttagcattt ... gtttgtttagATCCTGTTTGTTATATCAAAACCAGATGTTTTCAAGAG-CCCGACTTCTGA
EST: gi|193345380|gb|FK312959.1|FK312959
EST:     TGAAACCTGTCACAGGTGTCAGTCGTGTGACTGTTAAGAAGAGCAAAAAT                         ATCCTGTTTGTTATATCAAAACCAGATGTTTTCAAGAGCCCGACTTCTGAC
genomic: TGAAACCTGTCACAGGTGTCAGTCGTGTGACTGTTAAGAAGAGCAAAAATgttagcattt ... gtttgtttagATCCTGTTTGTTATATCAAAACCAGATGTTTTCAAGAGCCCGACTTCTGAC
EST: gi|120529122|gb|EH257256.1|EH257256
EST:     TGAAACCTGTCACAGGTGTCAGTCGTGTGACTGTTAAGAAGAGCAAAAAT                         ATCCTGTTTGTTATATCAAAACCAGATGTTTTCAAGAGCCCGACTTCTGAC
genomic: TGAAACCTGTCACAGGTGTCAGTCGTGTGACTGTTAAGAAGAGCAAAAATgttagcattt ... gtttgtttagATCCTGTTTGTTATATCAAAACCAGATGTTTTCAAGAGCCCGACTTCTGAC
EST: gi|192331245|gb|FK023756.1|FK023756
EST:     TGAAACCTGTCACAGGTGTCAGTCGTGTGACTGTTAAGAAGAGC-AAAAT                         ATCCTGTTTGTTATATCAAAACCAGATGTTTTCAAGAGCCCGACTTCTGAC
genomic: TGAAACCTGTCACAGGTGTCAGTCGTGTGACTGTTAAGAAGAGCAAAAATgttagcattt ... gtttgtttagATCCTGTTTGTTATATCAAAACCAGATGTTTTCAAGAGCCCGACTTCTGAC
EST: gi|19937243|gb|BQ081212.1|BQ081212
EST:     TGAAACCTGTCACAGGTGTCAGTCGTGTGACTGTTAAGAAGAGCAAAAAT                         ATCCTGTTTGTTATATCAAAACCAGATGTTTTCAAGAGCCCGACTTCTGAC
genomic: TGAAACCTGTCACAGGTGTCAGTCGTGTGACTGTTAAGAAGAGCAAAAATgttagcattt ... gtttgtttagATCCTGTTTGTTATATCAAAACCAGATGTTTTCAAGAGCCCGACTTCTGAC
EST: gi|208099271|gb|GD899220.1|GD899220
EST:     TGAAACCTGTCACAGGTGTCAGTCGTGTGACTGTTAAGAAGAGCAAAAAT                         ATCCTGTTTGTTATATCAAAACCAGATGTTTTCAAGAGCCCGACTTCTGAC
genomic: TGAAACCTGTCACAGGTGTCAGTCGTGTGACTGTTAAGAAGAGCAAAAATgttagcattt ... gtttgtttagATCCTGTTTGTTATATCAAAACCAGATGTTTTCAAGAGCCCGACTTCTGAC
EST: gi|120494539|gb|EH222706.1|EH222706
EST:     TTAAGAAGAGCAAAAAT                         ATCCTGTTTGTTATATCAAAACCAGATGTTTTCAAGAGCCCGACTTCTGAC
genomic: TTAAGAAGAGCAAAAATgttagcattt ... gtttgtttagATCCTGTTTGTTATATCAAAACCAGATGTTTTCAAGAGCCCGACTTCTGAC
EST: gi|193446090|gb|FK414469.1|FK414469
EST:     TGAAACCTGTCACAGGTGTCAGTCGTGTGACTGTTAAGAAGAGCAAAAAT                         ATCCTGTTTGTTATATCAAAACCAGATGTTTTCAAGAGCCCGACTTCTGAC
genomic: TGAAACCTGTCACAGGTGTCAGTCGTGTGACTGTTAAGAAGAGCAAAAATgttagcattt ... gtttgtttagATCCTGTTTGTTATATCAAAACCAGATGTTTTCAAGAGCCCGACTTCTGAC
EST: gi|193367408|gb|FK329532.1|FK329532
EST:     TGAAACCTGTCACAGGTGTCAGTCGTGTGACTGTTAAGAAGAGC-AAAAT                         ATCCTGTTTGTTATATCAAAACCAGATGTTTTCAAGAGCCCGACTTCTGAC
genomic: TGAAACCTGTCACAGGTGTCAGTCGTGTGACTGTTAAGAAGAGCAAAAATgttagcattt ... gtttgtttagATCCTGTTTGTTATATCAAAACCAGATGTTTTCAAGAGCCCGACTTCTGAC
EST: gi|7692485|gb|AW760590.1|AW760590
EST:     TGAAACCTGTCACAGGTGTCAGTCGTGTGACTGTTAAGAAGAGCAAAAAT                         ATCCTGTTTGTTATATCAAAACCAGATGTTTTCAAGAGCCCGACTTCTGAC
genomic: TGAAACCTGTCACAGGTGTCAGTCGTGTGACTGTTAAGAAGAGCAAAAATgttagcattt ... gtttgtttagATCCTGTTTGTTATATCAAAACCAGATGTTTTCAAGAGCCCGACTTCTGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcatctatttcgtacttgtcaatattgaatttatttctcctttgtttgtttagATCCTGTTTGTTATATCAAAACCAGATGTTTTCAAGAGCCCGACTTCTGACACATACATTATATTCGGCGAAGCCAAGATTGAAGACTTGAGCTCACAGC
                               tttatttctcctttgt  CT-rich tract
                 ttgtcaatattgaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagcatttgacatctatttattttgaagaacttttcattgtttcatctatttcgtacttgtcaatattgaatttatttctcctttgtttgtttagATCCTGTTTGTTATATCAAAACCAGATGTTTTCAAGAGCCCGACTTCTGACACATACATTATATTCGGCGAAGCCAAGATTGAAGACTTGAGCTCACAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA