Sequence
atgc intronic sequence ATGC exonic sequence...gtatgtgtgagtgtgtcaatggcttccaaattcttcttcatctaattattctatgctgttacgtgataataataaataacattggtgcaaaaataaacagATGCATATGTGGGGGCATGGATCTCAATATAGGAAGGGACCAGAGTCTCTAAGGGGAACACAACCCACGGCTATGCTAAGACTTCCTTGCTATTGCTGTG
Basic information
species | Glycine max |
transcript | GLYMA12G06080.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G06080.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv06s0004g01870.t01 (Vitis vinifera), 3'ss of exon 1
gtatgtgtgagtgtgtcaatggcttccaaattcttcttcatctaattattctatgctgttacgtgataataataaataacattggtgcaaaaataa--------acagATGCATATGTGGGGGCATGGATCTCAATATAGGAAGGGACCAGAGTCTCTAAGGGGAACACAACCCACGGCTATGCTAAGACTTCCTTGCTATTGCTGTG
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--------tccccagttaccaactcaaagtttcatatataattgaatgtatggttttggttttgtatgagactaatttaacttgccttcaaaatacctcatgctgtagATGCATATGTGGGGGCATGGATCTCAGTATAGAAAAGGGCCAGAGTCTCTGAGGGGAACACAGCCAACGGCCATGCTTAAACTCCCATGCTTTTGCTGTG
upper sequence: GLYMA12G06080.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S359_44V6.1 (Physcomitrella patens), 3'ss of exon 3
gtatgtgtgagtgtgtcaatggcttccaaattcttcttcatctaatt---attctatgctgttacgtgataataataaataacattggtgcaaaaataaacagATGCATATGTGGGGGCATGGATCTCAATATAGGAAGGGACCAGAGTCTCTAAGGGGAACACAACCCACGGCTATGCTAAGACTTCCTTGCTATTGCTGTG
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-tggatcagaagtccacagggatttgtttagattacctgatagaatccaggtgataaaaagtggggccacacttacaatgaac-cggatgtggga-tgtgtagATGCACATGTGGGGCCATGGATCCCAATATAGGAAAGGCCCTGAATCGCTTCGAGGAACCCAACCCACTGCCATGCTGAGGCTGGCATGCTACTGTTGCT
upper sequence: GLYMA12G06080.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ16937 (Selaginella moellendorffii), 3'ss of exon 1
---gtatgtg-tgagtgtgtcaatggcttccaaattcttcttcatctaattattctatgctgttacgtgataataataaataacattggtgcaaaaataaacagATGCATATGTGGGGGCATGGATCTCAATATAGGAAGGGACCAGAGTCTCTAAGGGGAACACAACCCACGGCTATGCTAAGACTTCCTTGCTATTGCTGTG
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gtcttccatgatcagagcatgcatttttctgaaaaaaaaatttaaaaaattatatga--cttaaaaatctcaattttctcttacct--gtgtgtgactgaacagATGCATATGTGGGGGCATGGATCCCAGTACCGCCGCGGCCCCGAGTCACTGCGCGGCACGCAGCCCACCGCAATGCTCCGGCTGCCCTGCTACTGCTGCG
upper sequence: GLYMA12G06080.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ25578 (Selaginella moellendorffii), 3'ss of exon 1
gtatgtgtgagtgtgtcaatggcttccaaattcttcttcatctaattattctatgctgttacgtgataataataaataacattggtgcaaaaataaacagATGCATATGTGGGGGCATGGATCTCAATATAGGAAGGGACCAGAGTCTCTAAGGGGAACACAACCCACGGCTATGCTAAGACTTCCTTGCTATTGCTGTG
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-----------------------gttcacttcttttcttttcttttgaaac--tgcaagttcaagacaaacttttatgtcctttgtttct---cttccagATGCATATGTGGGGGCATGGTTCTCAGTATCGGCGGGGACCAGAATCTTTGCGAGGTGCTCAGCCGACAGCCATGCTAAGGCTTCCATGCTACTGCTGCG
upper sequence: GLYMA12G06080.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ16056 (Selaginella moellendorffii), 3'ss of exon 1
--gtatgtgtgagtgtgtcaatggcttccaaattcttcttcatctaattattctatgctgttacgtgataataataaataacattggtgcaaaaataaacagATGCATATGTGGGGGCATGGATCTCAATATAGGAAGGGACCAGAGTCTCTAAGGGGAACACAACCCACGGCTATGCTAAGACTTCCTTGCTATTGCTGTG
| || | | || | ||||| | || || ||| | || | | | | | | || | ||| | | |||||||||||||||||||||||||||| || || | || || ||||| || | || || || ||||| || ||||| | || || ||||| ||||| |
atcagagcatgcatttttctgaagaaaaaaaatttaaaattatatacgtatccatgacttaaaaatctcatttttctcttacct--gtgtgtgactgaacagATGCATATGTGGGGGCATGGATCCCAGTACCGCCGCGGCCCCGAGTCACTGCGCGGCACGCAGCCCACCGCAATGCTCCGGCTGCCCTGCTACTGCTGCG
upper sequence: GLYMA12G06080.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ22315 (Selaginella moellendorffii), 3'ss of exon 1
gtatgtgtgagtgtgtcaatggcttccaaattcttcttcatctaattattctatgctgttacgtgataataataaataacattggtgcaaaaataaacagATGCATATGTGGGGGCATGGATCTCAATATAGGAAGGGACCAGAGTCTCTAAGGGGAACACAACCCACGGCTATGCTAAGACTTCCTTGCTATTGCTGTG
| | | ||| | | || ||| | | || || | || | || || |||||||||||||||||||| || ||||| ||| || ||||||||||||| | | || | || || || || |||||||| ||||| ||||| ||||| |
-------------------------gttcacttcttttcgtttctttcgaaactgcaagttcaagacaaacttctatgtcgtttgtttct---cttccagATGCATATGTGGGGGCACGGTTCTCAGTATCGGCGGGGACCAGAGTCTTTGCGAGGTGCTCAGCCGACAGCCATGCTAAGGCTTCCATGCTACTGCTGCG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttattctatgctgttacgtgataataataaataacattggtgcaaaaataaacagATGCATATGTGGGGGCATGGATCTCAATATAGGAAGGGACCAGAGTCTCTAAGGGGAACACAACCCACGGCTATGCTAAGACTTCCTTGCTATTGCTGTG
aaataac putative branch site (score: 2)
tgataataataaataa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtgtgagtgtgtcaatggcttccaaattcttcttcatctaattattctatgctgttacgtgataataataaataacattggtgcaaaaataaacagATGCATATGTGGGGGCATGGATCTCAATATAGGAAGGGACCAGAGTCTCTAAGGGGAACACAACCCACGGCTATGCTAAGACTTCCTTGCTATTGCTGTG
gtatgtg
- - - - gagtgtg
- - - - - - - - - - -gcttcca
- - - - - - - - - - - - - - - - cttcttc
- - - - - - - - - - - - - - - - - - - - - - - - - - -tgctgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ataaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tggtgca