Sequence
atgc intronic sequence ATGC exonic sequencegtaatctcagtcttatatgtagctctactattgtgtatgtcgctttacctttgtgagggctcttctgtttgcacatttgtttaagcagtgccttttccttttaatctagGCAACCATTTCTGGTGCCAAGTCCATGAAGGGTACTCCATATTGGATGGCTCCAGAAGTTATTCTCCAGACTGGGCATAGCTT
Basic information
species | Glycine max |
transcript | GLYMA03G39760.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G39760.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G064613_T03 (Zea mays), 3'ss of exon 6
gtaatctcagtcttatatgtagctctactattgtgtatgtcgctttacctttgtga-gggctcttctgtttgcacatttgtttaagcagtgccttttccttttaatctagGCAACCATTTCTGGTGCCAAGTCCATGAAGGGTACTCCATATTGGATGGCTCCAGAAGTTATTCTCCAGACTGGGCATAGCTT
|| || | || | ||| || ||| || | | | | | | ||| || | || | | | ||| ||| || | | ||||||||| ||| ||||||| | ||||| ||||| |||||||||||||| |||||||| ||| | | || || | |
------gcattcattattgaccttttaccatc-tgtcatccgtccatcatatatcatgtgcttttatccttcaataccactgtaattccatgcttgtcttctg---ctagGCAACTGCAACTGCTGCCAAGACGATGAAAGGTACCCCATATTGGATGGCACCAGAAGTCATTGTTGGAAGCGGTCACAATTG
upper sequence: GLYMA03G39760.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G09000.1 (Arabidopsis thaliana), 3'ss of exon 6
-------------------gtaatctcagtcttatat----gtagctctactattgtgtatgtcgctttacctttgtgaggg-ctcttctg------tttgcacatttgtttaa-gcagtgccttttccttttaatctagGCAACCATTTCTGGTGCCAAGTCCATGAAGGGTACTCCATATTGGATGGCTCCAGAAGTTATTCTCCAGACTGGGCATAGCTT
|| ||| ||||| | | | || || ||| | | ||| | | | || || | | | || | | ||||| | | || || ||||||| || || ||||||| || || ||||| || || ||||||||||||||||| ||||||||||| || ||||| ||||||||
gtaagtcaaaaaataatttgttttctacaaagtatattgcaggaagcattctgttctgtgtattctcttatttcttagttggtctagtataacatatccttcagagtgatttaatgtgattgacttgatttcatctctagGCTACGATGACTGGTGCAAAATCTATGAAAGGGACACCATATTGGATGGCTCCGGAAGTTATTCTTCAAACTGGACATAGCTT
upper sequence: GLYMA03G39760.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G54960.1 (Arabidopsis thaliana), 3'ss of exon 6
------------gtaatctcagtcttatatgt-agctctactattgtgtatgtcgcttt--acctttgtgagggctcttctgtttgcacatttgtttaagcagtgccttttcct---------tttaatctagGCAACCATTTCTGGTGCCAAGTCCATGAAGGGTACTCCATATTGGATGGCTCCAGAAGTTATTCTCCAGACTGGGCATAGCTT
|| |||| ||| || | || || ||| || | ||| | || | | | ||| | | | | || | | || | ||| ||||||| || ||||| |||||||| || ||||| || ||||| |||||||||||||||||||||||||| || || |||||||||||
gtaagtcaatttttagtctccaacttctacttcagtaaaaccattctgctctcagttttctagtcttattcaagtttttcatataatatactccttatcatgatttcgattaatatacttgagttttctctagGCTACTATTTCGGGTGCCAAATCTATGAAAGGAACTCCCTATTGGATGGCTCCAGAAGTTATTCTTCAAACCGGGCATAGCTT
upper sequence: GLYMA03G39760.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv14s0128g00430.t01 (Vitis vinifera), 3'ss of exon 6
gtaatctcagtcttatatgtagctctactattgtgtatgtcgctttacctttgtgagggctcttctgtttgcacatttgtttaagcagtgccttttccttttaatctagGCAACCATTTCTGGTGCCAAGTCCATGAAGGGTACTCCATATTGGATGGCTCCAGAAGTTATTCTCCAGACTGGGCATAGCTT
||| | | ||| | ||| | | | || | | | ||| | ||||||| || || | | | | || | | | || || ||||| |||||||| ||||||||||||||||| || || || |||||||||||||| ||||| ||||||||||| || ||||||||
gtacacactatctgctctgtgtttattcatttattcagttgacttaatttttgtgattactttt--gctcaaaatctcgtctgattgagacattgg----ttgccatagGCTACCATTTCAGGTGCCAAGTCCATGAAAGGCACCCCGTATTGGATGGCTCCGGAAGTCATTCTCCAGACAGGCCATAGCTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gagggctcttctgtttgcacatttgtttaagcagtgccttttccttttaatctagGCAACCATTTCTGGTGCCAAGTCCATGAAGGGTACTCCATATTGGATGGCTCCAGAAGTTATTCTCCAGACTGGGCATAGCTT
ttttaat putative branch site (score: 3)
ccttttccttttaatc CT-rich tract
atttgtttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatctcagtcttatatgtagctctactattgtgtatgtcgctttacctttgtgagggctcttctgtttgcacatttgtttaagcagtgccttttccttttaatctagGCAACCATTTCTGGTGCCAAGTCCATGAAGGGTACTCCATATTGGATGGCTCCAGAAGTTATTCTCCAGACTGGGCATAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT