Sequence
atgc intronic sequence ATGC exonic sequencegttaatctcctatcacctatatataatttcattgataattacctaagagtatatttcattatttctgtcatgtttgtgatatcagGCATTATCTGATCCTTACTTCACTGGCTTGGCGAACATGGACCGTGAACCATCCACTCAACCCATTTCAAAACTTGAGTTTGAATTTGAGAGAAGGAAAT
Basic information
species | Glycine max |
transcript | GLYMA05G33980.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G33980.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os01g45620.1 (Oryza sativa), 3'ss of exon 5
------gttaatctcctatcacctatata-taatt--tcattgataattacctaagagt-atatttcattatttc--tgtcatgtttgtgatatcagGCATTATCTGATCCTTACTTCACTGGCTTGGCGAACATGGACCGTGAACCATCCACTCAACCCATTTCAAAACTTGAGTTTGAATTTGAGAGAAGGAAAT
| | || ||| | ||| | |||| ||| || | |||| | | | | |||||| | | || || || |||| ||| | ||||| ||||| ||||| ||||| || ||| |||||||| | |||||||| |||||||| |||||||| ||||||||||||||
gtaggaatgtagctactagccagcatagagcaattgctcaaaaatgttattctaatattcgttatccattatactgatattatagttatgtgtcaagGCCTTAACAGATCCATACTTTACTGGATTGGCAAATTCGGAACGTGAACCCATAGCACAACCCATCTCAAAACTCGAGTTTGAGTTTGAGAGAAGGAAGC
upper sequence: GLYMA05G33980.1 (Glycine max), 3'ss of exon 6
lower sequence: AT3G18040.2 (Arabidopsis thaliana), 3'ss of exon 5
-------------------gttaatctcctatcacctatatataatttcattga-----taattac-ctaagagtatatttcattatttctgt-catgtttgtg-atat-cagGCATTATCTGATCCTTACTTCACTGGCTTGGCGAACATGGACCGTGAACCATCCACTCAACCCATTTCAAAACTTGAGTTTGAATTTGAGAGAAGGAAAT
|| ||| | || | | ||||||| | ||| | || ||| | |||||| | | ||| |||| |||| |||||| | | |||||||||||| ||| |||| ||| | || || |||||||| |||||||| ||| | ||||| |||||||| ||||| ||||||||
gttagctcctctatacttgttttttctagcgtttccacttcaaaatttcagagcagtttcaatcgctctcagaaaaggaaacattatatatacatgtgtgtgtgtatatacagGCACTGGCAGATCCTTACTTCTATGGTCTGGCAAACGTTGATCGGGAACCATCTACTCAACCGATTCCGAAACTCGAGTTTGAGTTTGAAAGAAGGAAGA
upper sequence: GLYMA05G33980.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv02s0087g00500.t01 (Vitis vinifera), 3'ss of exon 1
---------------------------gttaatctcctatca-----cctatatataatttcattgataatt-acctaagagtatatttcattatttctg----tcatgtttgtgatatc-------agGCATTATCTGATCCTTACTTCACTGGCTTGGCGAACATGGACCGTGAACCATCCACTCAACCCATTTCAAAACTTGAGTTTGAATTTGAGAGAAGGAAAT----------------------------------------
|| || | | || || | | | | ||| || | ||| | || | || || | || | ||| | || | |||| ||| |||||||||| || ||| |||| || | || |||||||| |||||||||||||||||||||||||||||||| ||||||||||||||||
gtaccatgcgtaaaaaaaaaaccatccattcccttctcacaaaaattccctgatgttaatccgttggctcttcaactactggaatgtctccttgcatttgatcctaatgatcgtccaactgttgaagaggccttagctgatccttattttgatggtttggaaaatgtagATCGTGAACCTTCCACTCAACCCATTTCAAAACTTGAGTTTGAGTTTGAGAGAAGGAAATTAACAAAAGATGATGTTAGGGAGTTAATATATCGAGAGAT
upper sequence: GLYMA05G33980.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv17s0000g02570.t01 (Vitis vinifera), 3'ss of exon 6
--------------------------------------gttaatctcctatcacctatatataatttcattgataattacctaagagtatatttcattatttctgt-catgtttgtgatatcagGCATTATCTGATCCTTACTTCACTGGCTTGGCGAACATGGACCGTGAACCATCCACTCAACCCATTTCAAAACTTGAGTTTGAATTTGAGAGAAGGAAAT
|||| | || | | ||| || | | | ||| || | | | ||| | || || | | ||||| || | ||||| ||| ||||||| || || ||| ||||| || | || |||||||| |||||||||||||||||||||||||||||||| ||||||||||||||||
gtaatagttggtaattctaatatttcgctacttcaaaatttaaattaaaattgtaaagaaatataatc-tagttgatttgggaacactgtgcttcctaatatcattgcgtgtttatgttggcagGCTTTAGCTGATCCGTATTTTGATGGTTTGGCAAATGTAGATCGTGAACCTTCCACTCAACCCATTTCAAAACTTGAGTTTGAGTTTGAGAGAAGGAAAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attgataattacctaagagtatatttcattatttctgtcatgtttgtgatatcagGCATTATCTGATCCTTACTTCACTGGCTTGGCGAACATGGACCGTGAACCATCCACTCAACCCATTTCAAAACTTGAGTTTGAATTTGAGAGAAGGAAAT
cattgat putative branch site (score: 4)
taagagtatatttcat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttaatctcctatcacctatatataatttcattgataattacctaagagtatatttcattatttctgtcatgtttgtgatatcagGCATTATCTGATCCTTACTTCACTGGCTTGGCGAACATGGACCGTGAACCATCCACTCAACCCATTTCAAAACTTGAGTTTGAATTTGAGAGAAGGAAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA