Sequence
atgc intronic sequence ATGC exonic sequencegtatacccaaataaatattttatttgtaatctttacagcaaaaaggttgctcctttaacacggatatgttgcagATGGATGTATTTAATACTTTCATTGAGCTCTTGCGTCAAACTGGAAATGTCACAAAAGGGCAGATTGATGCAGATGAAATGAGGCAA
Basic information
species | Glycine max |
transcript | GLYMA17G00570.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G00570.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G168629_T04 (Zea mays), 3'ss of exon 10
gtatacccaaataaatattttatttgtaatctttacagcaaaaaggttgctcctttaacacggatatg-ttgcagATGGATGTATTTAATACTTTCATTGAGCTCTTGCGTCAAACTGGAAATGTCACAAAAGGGCAGATTGATGCAGATGAAATGAGGCAA
|| | || | | || || ||| | ||| | || | | | || | || |||||||| ||||||| || ||||||||||| || || |||||||| ||||| || ||||| || || ||||| ||
--gtaaatacatgataaattcatatgtgaaacttattattttctaaat-cttatgaagcttctatccgattctagATGGATATATTTAACACCTTCATTGAGCTGTTACGCCAAACTGGTAATGTTACGAAAGGACAAGGCGACATCGATGAGTCCAG----
upper sequence: GLYMA17G00570.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G053644_T02 (Zea mays), 3'ss of exon 8
gtatacccaaataaatattttatttgtaat-ctttacagcaaaaaggttgctcctttaacacggatatg-ttgcagATGGATGTATTTAATACTTTCATTGAGCTCTTGCGTCAAACTGGAAATGTCACAAAAGGGCAGATTGATGCAGATGAAATGAGGCAA
|| | || | | || | ||||| ||| | | | || | | | || | || |||||||| ||||||| || ||||||||||| || || |||||||| ||||| || ||||| || || ||||| ||
--gtaaatacatgataaattcgtatgtaaaacttcttattttctaaat--cttatgaagcttctatccgattctagATGGATATATTTAACACCTTCATTGAGCTGTTACGCCAAACTGGTAATGTTACGAAAGGACAAGGCGACATCGATGAGTCCAG----
upper sequence: GLYMA17G00570.1 (Glycine max), 3'ss of exon 9
lower sequence: AT2G02560.1 (Arabidopsis thaliana), 3'ss of exon 10
gtatacccaaataaatattttatt--tgtaatctt-tacagcaaaaaggttgctcctttaacacggatat------gttgcagATGGATGTATTTAATACTTTCATTGAGCTCTTGCGTCAAACTGGAAATGTCACAAAAGGGCAGATTGATGCAGATGAAATGAGGCAA
|| || | ||| ||| | | || |||| |||| | |||| | | ||| || || | ||| |||||||||||||| || || |||||||| || ||||| ||||| |||||||| |||||||| || | ||| | |||||| ||
--gtatgtaatttaatccattaatgctctattcttgctttgcaatatggttattgatctaagactgaggtactgttgttacagATGGATGTATTCAACACATTCATTGATCTGTTGCGGCAAACGGGAAATGTTACAAAAGGTCAAACTGACACCGATGAATCAAG----
upper sequence: GLYMA17G00570.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv12s0035g01840.t01 (Vitis vinifera), 3'ss of exon 11
gtatacccaaataaatattttatttgtaatc--tttacagcaaaaa-ggttgctcctttaacacggatatgttgcagATGGATGTATTTAATACTTTCATTGAGCTCTTGCGTCAAACTGGAAATGTCACAAAAGGGCAGATTGATGCAGATGAAATGAGGCAA
||| || ||| || ||||| || | ||| | | | | ||||| || | | ||| | ||||||||||| || ||||| || |||||||| | || |||||||||||||| || |||||||||| ||| ||||| ||||
gtaagccaaaaatgttaatttatagatatttgttttcctctatacatggttgatcatctggttttttcatgattcagATGGATGTGTTCAATACATTTATTGAGCTACTACGCCAAACTGGAAATGTTACGAAAGGGCAGACTGACATGAATGAACTGAG---- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttatttgtaatctttacagcaaaaaggttgctcctttaacacggatatgttgcagATGGATGTATTTAATACTTTCATTGAGCTCTTGCGTCAAACTGGAAATGTCACAAAAGGGCAGATTGATGCAGATGAAATGAGGCAA
ctttaac putative branch site (score: 3)
taatcttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatacccaaataaatattttatttgtaatctttacagcaaaaaggttgctcctttaacacggatatgttgcagATGGATGTATTTAATACTTTCATTGAGCTCTTGCGTCAAACTGGAAATGTCACAAAAGGGCAGATTGATGCAGATGAAATGAGGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG