Sequence
atgc intronic sequence ATGC exonic sequencegtaagttgtaatgtaactgtaaatgacaatgttctacctcatttgtctaacgttttacttaaaaaaatatttctaacaccattttcttgctcttttatttaataacagACATTATTAGCAAAAGCTGTTGCTACAGAGTGCTCCTTAAATTTTCTTAGTGTGAAAGGTCCTGAACTGATCAACATGTACATTGGAGAGTCTGAAAAGA
Basic information
species | Glycine max |
transcript | GLYMA19G39580.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G39580.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os04g52690.3 (Oryza sativa), 3'ss of exon 9
------------------------------gtaagttgtaatgtaactgtaaatgacaatgttctacctcatttgtctaacgttt-----tacttaaaaaaatatttctaacaccattttcttgctcttttatttaataacagACATTATTAGCAAAAGCTGTTGCTACAGAGTGCTCCTTAAATTTTCTTAGTGTGAAAGGTCCTGAACTGATCAACATGTACATTGGAGAGTCTGAAAAGA
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gttggtttacggtgtttttctattttatactttgtttttagttaagctttacctttt--cgtttcttcccatctgtccaaagaggataagcacatagaaaagcactgtatacgtgctcattattattatgtttcaatttgcagACATTATTGGCAAAAGCTGTAGCAACAGAGTGCTCTTTAAACTTTCTTAGTGTAAAAGGTCCAGAATTGATTAACATGTATGTTGGAGAATCGGAGAAGA
upper sequence: GLYMA19G39580.1 (Glycine max), 3'ss of exon 9
lower sequence: AT1G03000.1 (Arabidopsis thaliana), 3'ss of exon 8
gtaagttgtaatgtaactgtaaatga-caatgttctacctcatttgtctaacgttttacttaaaaaaatatttctaacaccattttcttgctcttttatttaata-acagACATTATTAGCAAAAGCTGTTGCTACAGAGTGCTCCTTAAATTTTCTTAGTGTGAAAGGTCCTGAACTGATCAACATGTACATTGGAGAGTCTGAAAAGA
|||| | | | || || | ||| || | | | ||| | | || | ||||| | | || ||| ||| |||||| ||| | ||||||||||| || |||||||||||||||||||| || ||||| || ||||| ||| | ||||||||||| ||||||||||| || || |
------------------gtaagtaagccattttttctttcacttttagcatctcttaatagtctgttttttggcagttatatttttgagtttttgaattaaatttacagACTTTACTGGCAAAAGCTGTGGCGACAGAGTGCTCCTTAAATTTCCTCAGTGTAAAGGGTCCAGAATTAATCAACATGTATATTGGAGAGTCAGAGAAAA
upper sequence: GLYMA19G39580.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv07s0104g01610.t01 (Vitis vinifera), 3'ss of exon 9
gtaagttgtaatgt---aactgtaaatgacaatgttc---tacctcattt---gtctaacgttttacttaaaaaaatatttctaacaccattttcttgctcttttatttaataacagACATTATTAGCAAAAGCTGTTGCTACAGAGTGCTCCTTAAATTTTCTTAGTGTGAAAGGTCCTGAACTGATCAACATGTACATTGGAGAGTCTGAAAAGA
||||||| | | | | | ||| || | ||| | |||| || || ||||| | || | ||| || || ||| | | ||| ||||| ||||| |||||||||||||| |||||||||||| | |||||||| ||||| ||||| |||||||||||||||||||| || ||||| || || || |
gtaagtttttgtttgttagccacttatggtgatatctcaatacgttatttcttgtttatttttttaaccaggaacctggttcattgctttcttggttactcctattgcaaatctcagACTTTATTGGCAAAAGCTGTTGCAACAGAGTGCTCCCTCAATTTTCTGAGTGTAAAAGGGCCTGAACTGATCAACATGTATATAGGAGAATCAGAGAAAA
upper sequence: GLYMA19G39580.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S68_6V6.1 (Physcomitrella patens), 3'ss of exon 10
------------------------------gtaagttgtaatgtaactgtaaatgaca--atgttctacct----catttgtctaacgttttac-ttaaaaaaat---atttc-taac---accattttcttgctcttttattta-ataacagACATTATTAGCAAAAGCTGTTGCTACAGAGTGCTCCTTAAATTTTCTTAGTGTGAAAGGTCCTGAACTGATCAACATGTACATTGGAGAGTCTGAAAAGA
| || | || | |||| | | || | |||| | | || | || || ||| | || | | || | | || | | | | ||| | |||||||| | || || |||||||| || |||||| | || || ||||| ||||| ||||||||||| || ||||||||||||||||||||||| || ||||
gtataagataatttcgagctcattagacatgctgactgcggttgtgctttttatgatagaaagtcttgttctgaacattaggcaaattatcaacactaccaaagtttggttgcatgactgaatcgattatgtaccgtgatgtttgtgttgcagACATTGCTCGCCAAGGCTGTTGCCACTGAGTGCGCGTTGAACTTTCTGAGTGTCAAAGGTCCTGAGCTCATCAACATGTACATTGGAGAGTCAGAGAAGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttacttaaaaaaatatttctaacaccattttcttgctcttttatttaataacagACATTATTAGCAAAAGCTGTTGCTACAGAGTGCTCCTTAAATTTTCTTAGTGTGAAAGGTCCTGAACTGATCAACATGTACATTGGAGAGTCTGAAAAGA
ccattttcttgctctt CT-rich tract
ttaaaaaaatatttct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagttgtaatgtaactgtaaatgacaatgttctacctcatttgtctaacgttttacttaaaaaaatatttctaacaccattttcttgctcttttatttaataacagACATTATTAGCAAAAGCTGTTGCTACAGAGTGCTCCTTAAATTTTCTTAGTGTGAAAGGTCCTGAACTGATCAACATGTACATTGGAGAGTCTGAAAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA