Sequence
atgc intronic sequence ATGC exonic sequencegttagtatttcctcgtgatcttgtttctgttagttttttttttttttttgtcagctacttttctgttagctgaagttggtattattgaaatccaagttggtcggctccttttctcttaatataagattgtaatgttcgcctgtcttgcttctttagTGACATTAACATGATGATGGTTGGCGATCCCTCTGTTGCCAAGTCTCAACTCTTGAGAGCAATTATGAACATTGCTCCCTTGGCCATATCAACCACAGGC
Basic information
species | Glycine max |
transcript | GLYMA05G25980.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G25980.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os05g39850.1 (Oryza sativa), 3'ss of exon 6
gttagtatttcctcgtgatcttgtttctgttagttttttttttttttttgtcagctacttttctgttagctgaagttggtattattgaaatccaagttggtcggctccttttctcttaatataagattgtaatgttcgcctgtcttgcttctttagTGACATTAACATGATGATGGTTGGCGATCCCTCTGTTGCCAAGTCTCAACTCTTGAGAGCAATTATGAACATTGCTCCCTTGGCCATATCAACCACAGGC
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----------------------------------------------------------gtcagtgctgtttc---ttcgtatcattgcttctgttgtaacttgctttcaatgattgtagtgtaaatatatcttacttatgtggtatgc------agAGATATAAACATGATGATGGTAGGAGATCCTTCAGTTGCCAAGTCCCAGCTCCTAAGAGCGGTTATGAACATTGCCCCTTTGGCTATTTCAACTACTGGA
upper sequence: GLYMA05G25980.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G162445_T01 (Zea mays), 3'ss of exon 6
gttagtatttcctcgtgatcttgtttctgttagttttttttttttttttgtcagctacttttctgttagctgaagttggtattattgaaatccaagttggtcggctccttttctcttaatataagattgtaatgttcgcctgtcttgcttctttagTGACATTAACATGATGATGGTTGGCGATCCCTCTGTTGCCAAGTCTCAACTCTTGAGAGCAATTATGAACATTGCTCCCTTGGCCATATCAACCACAGGC
| | || | || | | ||| | | ||| | | | | ||| | || | | ||| ||| || || || |||||||||||||| || ||||| || ||||||||||| || ||| | ||||| | |||||||||||||| ||||| |||||||| || |||
-----------------------------------------------------------------------gtaagtgatgtt--tcagatcattacagatacatgattttgttgattgtgttttatttatttatttctatattttggctctc-agAGATATAAACATGATGATGGTGGGAGATCCTTCAGTTGCCAAGTCCCAGCTCCTAAGAGCTGTCATGAACATTGCTCCTTTGGCTATATCAACAACTGGC
upper sequence: GLYMA05G25980.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G100639_T01 (Zea mays), 3'ss of exon 6
gttagtatttcctcgtgatcttgtttctgttagttttttttttttttttgtcagctacttttctgttagctgaagttggtattattgaaatccaagttggtcggctccttttctcttaatataagattgtaatgttcgcctgtcttgcttctttagTGACATTAACATGATGATGGTTGGCGATCCCTCTGTTGCCAAGTCTCAACTCTTGAGAGCAATTATGAACATTGCTCCCTTGGCCATATCAACCACAGGC
| || | | | | ||| ||| | | || | || ||| | ||| || | | ||| | || || || |||||||||||||| || ||||| || ||||||||||| || ||| | ||||| | ||||||||||| || ||||| || ||||| || |||
----------------------------------------------------------gtaagtgatgtttcagatc---attgctgatacatgatttaattaataatgctttatttattcatccatt----catttctatattttggca-tacagAGATATAAACATGATGATGGTGGGAGATCCTTCAGTTGCCAAGTCCCAGCTCCTAAGAGCTGTCATGAACATTGCCCCTTTGGCTATCTCAACAACTGGC
upper sequence: GLYMA05G25980.1 (Glycine max), 3'ss of exon 6
lower sequence: AT5G46280.1 (Arabidopsis thaliana), 3'ss of exon 6
gttagtatttcctcgtgatcttgtttctgttagttttttttttttttttgtcagctacttttctgttagctgaagttggtattattgaaatccaagttggtcggctccttttctcttaatataagattgtaatgttcgcctgtcttgcttctttagTGACATTAACATGATGATGGTTGGCGATCCCTCTGTTGCCAAGTCTCAACTCTTGAGAGCAATTATGAACATTGCTCCCTTGGCCATATCAACCACAGGC
| | || ||| | | ||| || | | | | || | || || || | | || | |||| | | | | | ||||| || || ||||| ||||||||||||||||| ||||| ||||||||||| |||||||| ||||||| || ||||| ||||| || ||||| |||||||||||||||
------------------------------------gtaagtcttgcttgaaaacagatttcagattcgactcattggatactttttg--tctaactca------tttttctttcttcacttgaaaacaaa-----------tcttgtgctttcagAGACATCAACATGATGATGGTTGGTGATCCATCTGTTGCCAAATCTCAACTTCTGAGAGCGATAATGAATATTGCACCTTTGGCTATATCAACCACAGGC
upper sequence: GLYMA05G25980.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv10s0003g03080.t01 (Vitis vinifera), 3'ss of exon 6
gttagtatttcctcgtgatcttgtttctgttagttttttttttttttttgtcagctacttttctgttagctgaagttggta-ttattgaaatccaagttggtcggctccttttctcttaatataagattgtaatgttcgcctgtcttgcttctt-tagTGACATTAACATGATGATGGTTGGCGATCCCTCTGTTGCCAAGTCTCAACTCTTGAGAGCAATTATGAACATTGCTCCCTTGGCCATATCAACCACAGGC
| | | | | | | ||| | | || | | || || || || | || ||||||| || | | ||| ||||| | ||| ||||||||| ||||||||||||||||| ||||| || ||||||||||||||||| || |||||||||||||| |||||||| ||||| ||||| ||||| ||
-----------------------------------------tcgctcctccgacttgttctattgtgggtcatatctgaaagctcctgtcataaaa-----tcaaatttttacatcttaat--aaaaccg-aat---------tcttgttccttatagTGACATAAACATGATGATGGTTGGTGATCCTTCCGTTGCCAAGTCTCAACTGTTAAGAGCAATTATGAATATTGCTCCTTTGGCTATATCTACCACTGGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cggctccttttctcttaatataagattgtaatgttcgcctgtcttgcttctttagTGACATTAACATGATGATGGTTGGCGATCCCTCTGTTGCCAAGTCTCAACTCTTGAGAGCAATTATGAACATTGCTCCCTTGGCCATATCAACCACAGGC
tcttaat putative branch site (score: 3)
cctgtcttgcttcttt putative PPT
ttaatataagattgta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagtatttcctcgtgatcttgtttctgttagttttttttttttttttgtcagctacttttctgttagctgaagttggtattattgaaatccaagttggtcggctccttttctcttaatataagattgtaatgttcgcctgtcttgcttctttagTGACATTAACATGATGATGGTTGGCGATCCCTCTGTTGCCAAGTCTCAACTCTTGAGAGCAATTATGAACATTGCTCCCTTGGCCATATCAACCACAGGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA