Sequence
atgc intronic sequence ATGC exonic sequence...catgtcatgtagagattagtagaaaccatataatgatttctctctttttctttaaggctatatattttgacagtgttcaaaaaaatgaaccaattcacagGTGGGCTGCTATAGCCTCTCAGCTACCAGGAAGAACAGACAATGAGATAAAAAACTTATGGAACACCCACTTGAAGAAACGTCTCATTTGCATGGGCCTT
Basic information
species | Glycine max |
transcript | GLYMA03G01540.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G01540.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G61250.1 (Arabidopsis thaliana), 3'ss of exon 2
catgtcatgtagagattagtagaaaccatataatgatttctctctttttctttaaggctatatattttgacagtgttcaaaa---aaatgaaccaatt--cacagGTGGGCTGCTATAGCCTCTCAGCTACCAGGAAGAACAGACAATGAGATAAAAAACTTATGGAACACCCACTTGAAGAAACGTCTCATTTGCATGGGCCTT
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---------------gtcttttactttgcttctccaccttccttctctactcta--gctatcttcttcttcattgtctgaattctgcttttttttgtttcctcagGTGGGCTGCTATTGCAGCACAGCTTCCAGGAAGAACAGACAACGAGATCAAGAACTTATGGAACACTCATTTGAAGAAACGTCTTTTATCTATGGGTCTT
upper sequence: GLYMA03G01540.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv15s0046g03190.t01 (Vitis vinifera), 3'ss of exon 2
catgtcatgtagagattagtagaaaccat-ataatgatttctctctttttctttaaggctatatattttgacagtgttcaaaaaaatgaacca--attcacagGTGGGCTGCTATAGCCTCTCAGCTACCAGGAAGAACAGACAATGAGATAAAAAACTTATGGAACACCCACTTGAAGAAACGTCTCATTTGCATGGGCCTT
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---ctttggttaggttttctgcaatttgtcactctgacattgatggaatattttcatatttcatgttatgaacttttaacaatacttgatacactatgttcagGTGGGCTGCCATTGCCTCTCAACTGCCCGGAAGGACCGATAATGAGATCAAGAACCTATGGAACACCCACTTGAAGAAGCGCCTGCTTGGAATGGGGCTT
upper sequence: GLYMA03G01540.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S1_78V6.1 (Physcomitrella patens), 3'ss of exon 2
----------------------------------------------------------------------------catgtcatgtagagattagtagaaa---ccatataatgatttctctctttttctttaaggctata-tattttga-cagtg-ttcaaaaaaatgaaccaattc-acagGTGGGCTGCTATAGCCTCTCAGCTACCAGGAAGAACAGACAATGAGATAAAAAACTTATGGAACACCCACTTGAAGAAACGTCTCATTTGCATGGGCCTT
| ||||| | | || |||| | | | | | | | | || || | |||||| | || || | || || ||| ||| | |||||||| ||| || || | | || ||||| ||||||||||||| |||||||| ||||||||||| ||||| | ||||| ||
gtgatgcctctaactgttataaaaccctctaattctgatccttctgtaacattgttggtgcgatcgtcttggcggtgttttcatgacgctttcgacgcgaagttccatgtggtagccttcttttgtaacaatgcggacctagtgttttgaacgatggctctggttattgtgttttttttgcagATGGTCAGCTATAGCTAGTCATCTTCCTCGCCGCACTGACAACGAGATAAAAAACTACTGGAACACTCACTTGAAGAAGCGTCTGCTGCAAATGGGGATT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttctttaaggctatatattttgacagtgttcaaaaaaatgaaccaattcacagGTGGGCTGCTATAGCCTCTCAGCTACCAGGAAGAACAGACAATGAGATAAAAAACTTATGGAACACCCACTTGAAGAAACGTCTCATTTGCATGGGCCTT
ttttgac putative branch site (score: 3)
tatatattttgaca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
catgtcatgtagagattagtagaaaccatataatgatttctctctttttctttaaggctatatattttgacagtgttcaaaaaaatgaaccaattcacagGTGGGCTGCTATAGCCTCTCAGCTACCAGGAAGAACAGACAATGAGATAAAAAACTTATGGAACACCCACTTGAAGAAACGTCTCATTTGCATGGGCCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
catgtca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agtgttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaaa