Sequence
atgc intronic sequence ATGC exonic sequencegtcagcactcagcacattagaagatttgtttcatgcatgcctcttaaattatgttcctgaactcaattttttttttttggtaataagggtatagtcacaagtacacttgttaataatcgctgttagaattttttgtacagTGGTGAGAGTGGATCTGGGAAAACAGAGACAGCAAAAATTGCTATGCAATACTTAGCTGCTCTTGGTGGTGGCTGTTCTGGAATAGAAAATGAAGTTCTT
Basic information
species | Glycine max |
transcript | GLYMA13G35790.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G35790.1 (Glycine max), 3'ss of exon 7
lower sequence: AT4G27370.1 (Arabidopsis thaliana), 3'ss of exon 5
gtcagcactcagcacattagaagatttgtttcatgcatgcc-tcttaaattatgttcctgaactcaattttttttttttggtaataagggtatagtcacaagtacacttgttaataatcg--ctgttagaatttt-ttgtacagTGGTGAGAGTGGATCTGGGAAAACAGAGACAGCAAAAATTGCTATGCAATACTTAGCTGCTCTTGGTGGTGGCTGTTCTGGAATAGAAAATGAAGTTCTT
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---------------------------gtacgatgctttctattctgaatgctttttgtgcact-gataatttgactatgcatatgtgaaggtgacttctgatattcatatcatcaatcaaatgaataaaatattatttcttagTGGAGAAAGTGGAGCTGGGAAAACTGAGACAGCAAAATATGCAATGCAGTACTTGGAAGCTCTTGGTGGAGGTAGCTTTGGGGTGGAAAATGAAATCCTA
upper sequence: GLYMA13G35790.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv19s0014g03640.t01 (Vitis vinifera), 3'ss of exon 6
gtcagc--actcagcacattagaagatt--tgtttcatgcatgcctcttaaattatgttcctg----aactcaattttttttttttg-gtaataagggtatagtcacaagtacacttgttaataa--tcgctgttagaatttt-ttgtacagTGGTGAGAGTGGATCTGGGAAAACAGAGACAGCAAAAATTGCTATGCAATACTTAGCTGCTCTTGGTGGTGGCTGTTCTGGAATAGAAAATGAAGTTCTT
||||| | | || | || ||| ||| || |||| | || | ||| | || ||| | ||| || | || | || | || | | | || || | | | |||||| | | |||||| || | ||| |||| ||||| ||||||||||||||||| ||||||||| | ||||| |||||||| ||| | ||| ||||| |||||| | |
gtcagttggagtatcttcctatcattttactgtaaaatgggagcttctttatggatacttctgttgcagttcgttttcaatgtttaatatattgagcctttaagcccatttttagtgtttcatgaggtgatcatcgaaattttatcttccagTGGCGAAATTGGTGCTGGAAAAACTGAGACAGCAAAAATTGCAATGCAATACCTGGCTGCACTTGGTGGAGGCAGCGATGGGATAGAGAATGAACTCACT
upper sequence: GLYMA13G35790.1 (Glycine max), 3'ss of exon 7
lower sequence: PP1S104_215V6.1 (Physcomitrella patens), 3'ss of exon 5
------------------gtcagcactcagcaca--ttagaagatttgtttca-tgcatgcctcttaaattatgttcctgaactcaatttttttt--ttttggtaataagggtatagtcacaagtacacttgttaataatcgc-tgttagaattttttgtacagTGGTGAGAGTGGATCTGGGAAAACAGAGACAGCAAAAATTGCTATGCAATACTTAGCTGCTCTTGGTGGTGGCTGTTCTGGAATAGAAAATGAAGTTCTT---
|| || | | | | |||| | ||| | | ||||| ||| | | || |||| ||| | || || || | | | | || | | | || | || | |||| ||||||||||||||||||| | ||||||||||| || ||||| ||||| ||||| || ||||||||||| || || || || || |||||| ||||| || |
gtaatttgtatatctttgttctacattttgttctgttccaaagaagaatctcaatttttttaatttaaagaatggccggaatctgcatttatttaaacactagttattagtattctcttcaatggtcatctcatgaaaacaacatgcttattttttgtgtacagTGGTGAGAGTGGTGCAGGGAAAACAGAAACGGCAAAGATTGCCATGCAGTATTTAGCTGCTCTAGGAGGAGGTAGT---GGGATAGAAGATGAAATTTTGCAA
upper sequence: GLYMA13G35790.1 (Glycine max), 3'ss of exon 7
lower sequence: PP1S199_21V6.1 (Physcomitrella patens), 3'ss of exon 5
-----------gtcagcactcagcacattagaagattt---gtttcatgcatgcctcttaaattatgttcctgaactcaattttttttttttggtaataagggtatagtcacaagtacacttgttaataatcgctgttagaattttttgtacagTGGTGAGAGTGGATCTGGGAAAACAGAGACAGCAAAAATTGCTATGCAATACTTAGCTGCTCTTGGTGGTGGCTGTTCTGGAATAGAAAATGAAGTTCTT---
| | || | | || | ||| | | | || || || || || || | ||| | | | | | || || | || | | | | | | | | | ||||||||||||||||||| | || || ||||| || ||||| ||||||||||| || || |||||||| || || || || ||||||||| ||||| || |
gtagtttatgtcccttgattcggtgctatattaattttcaaactacgagtatcttcttttgttttcaatcagcgaccacgttgtgcatttatttagacagtgtcctcttcgatagc-tatatgatgtacacggttttcatattactgtgtacagTGGTGAGAGTGGCGCAGGTAAGACAGAAACGGCAAAGATTGCTATGCAGTATTTGGCTGCTCTAGGAGGAGGTAGT---GGAATAGAAGATGAAATTTTACAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agggtatagtcacaagtacacttgttaataatcgctgttagaattttttgtacagTGGTGAGAGTGGATCTGGGAAAACAGAGACAGCAAAAATTGCTATGCAATACTTAGCTGCTCTTGGTGGTGGCTGTTCTGGAATAGAAAATGAAGTTCTT
tgttaat putative branch site (score: 3)
ttttttgt putative PPT
ttagaattttttgta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcagcactcagcacattagaagatttgtttcatgcatgcctcttaaattatgttcctgaactcaattttttttttttggtaataagggtatagtcacaagtacacttgttaataatcgctgttagaattttttgtacagTGGTGAGAGTGGATCTGGGAAAACAGAGACAGCAAAAATTGCTATGCAATACTTAGCTGCTCTTGGTGGTGGCTGTTCTGGAATAGAAAATGAAGTTCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT