Sequence
atgc intronic sequence ATGC exonic sequence...gatgatagtgtaaaaaatctttccacattctaatcaaattaatttccgaatgtccaactagttctgtaactctgtcactatgttctttgctcattaatagTGGAACTTTCGTATTGGATTCACTCCTAGAGAAGGTTTGGTTATATATTCGGTTGCATATATTGATGGTAGTCAAGGGCGAAGGCCTGTAGCACATAGAC
Basic information
species | Glycine max |
transcript | GLYMA17G09290.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G09290.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os04g04950.1 (Oryza sativa), 3'ss of exon 5
gatgatag--tgtaaaaaatctttccacattctaatcaaattaatttccgaatgtccaactagttctgtaactctgtcactatgttctttgctcattaatagTGGAACTTTCGTATTGGATTCACTCCTAGAGAAGGTTTGGTTATATATTCGGTTGCATATATTGATGGTAGTCAAGGGCGAAGGCCTGTAGCACATAGAC
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gttaactggctatctatagtgtttac-tgttttaatttaattattggcgtagtagt-atctaata----aaaatgattaaaaaaacattttctgttgaacagTGGAACTTTCGTATTGGCTTCACCCCTAAAGAAGGTTTAGTTCTTCATTCTGTTGCATATGTTGATGGAAACCGTGGCCGTCGACCTATCGCTCACAGGC
upper sequence: GLYMA17G09290.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G147884_T01 (Zea mays), 3'ss of exon 5
gatgatagtgtaaaaaatctttccacattctaatcaaattaatttccgaatgtccaactagttctgtaactctgtcactatgttctttgctcattaatagTGGAACTTTCGTATTGGATTCACTCCTAGAGAAGGTTTGGTTATATATTCGGTTGCATATATTGATGGTAGTCAAGGGCGAAGGCCTGTAGCACATAGAC
| | | | || | | | | | | | || | | | | | || | || |||||||||| |||||||| ||||| || | ||| ||||||||||| ||||| ||||| ||| |||||||||| | || || || ||| |||||||||| |
----------------------gtaattgtttgttgaactgcagtgctagtattaacataatgtcttctgaaataaataacacttaatggttat-ggcagTGGAACTTCCGTATTGGCTTCACCCCCAAAGAGGGTTTGGTTATCTATTCTGTTGCTTATGTTGATGGTAGCCGTGGACGTAGACCTATAGCACATAGGC
upper sequence: GLYMA17G09290.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv17s0000g09100.t01 (Vitis vinifera), 3'ss of exon 5
--gatgatagtgtaaaaaatctttccacattctaatcaaattaatttccgaatgtccaactagttctgtaactctgtcactatgttctttgctca-ttaatagTGGAACTTTCGTATTGGATTCACTCCTAGAGAAGGTTTGGTTATATATTCGGTTGCATATATTGATGGTAGTCAAGGGCGAAGGCCTGTAGCACATAGAC
| | || | | ||| |||||| || || | |||| ||| || ||| | | || | | | || ||||||| || |||||||| |||||||| ||||| ||||||||||| |||| ||||||||| |||||||||||| || ||||| |||||||| |||||
gtacttttggtttcttgagctggcttgttaataaatgtaattaaagtcagagatgcatacta-------aacactatcaatgttttatctttttggttggcagTGGAATTTCCGTATTGGTTTCACTCCCAGAGAGGGTTTGGTTATCCATTCTGTTGCATATGTTGATGGTAGTCGGGGTCGAAGACCTGTAGCTCATAGGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccgaatgtccaactagttctgtaactctgtcactatgttctttgctcattaatagTGGAACTTTCGTATTGGATTCACTCCTAGAGAAGGTTTGGTTATATATTCGGTTGCATATATTGATGGTAGTCAAGGGCGAAGGCCTGTAGCACATAGAC
ctgtaac putative branch site (score: 3)
ttctttgctc putative PPT
tcattaata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gatgatagtgtaaaaaatctttccacattctaatcaaattaatttccgaatgtccaactagttctgtaactctgtcactatgttctttgctcattaatagTGGAACTTTCGTATTGGATTCACTCCTAGAGAAGGTTTGGTTATATATTCGGTTGCATATATTGATGGTAGTCAAGGGCGAAGGCCTGTAGCACATAGAC
- -gatagtg
- - - - - -aaaaaat
- - - - - - - - - - - -cacattc
- - - - - - - - - - - - - - - - - - - - - - - - - - -ccaacta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttctgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgtcac