Sequence
atgc intronic sequence ATGC exonic sequence...ttttatctgagatcaataattaatttgcatgctagacatgtctttatgctgattggtcatttatctgcagtgcttatgtctatcttttgaatctttgcagCGTTTTGCTGCTGTTATTATGAGGATCAGGGAACCAAAAACTACTGCACTCATTTTTGCATCTGGCAAGATG
Basic information
species | Glycine max |
transcript | GLYMA09G41330.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G41330.2 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os03g45410.1 (Oryza sativa), 3'ss of exon 3
ttttatctgagat-caataattaatttgcatgctagacatgtctttatgctgattgg---tcatttat-ctgcagtgcttatgtctatcttttgaatctttgcagCGTTTTGCTGCTGTTATTATGAGGATCAGGGAACCAAAAACTACTGCACTCATTTTTGCATCTGGCAAGATG
|| ||| | || || | | | || ||| || || || || ||| | | |||||| | ||| | || ||| | | |||||||||||||| ||||| ||||| || || |||||||||||||| || || || |||||||| || || |||
cttagattgatttacactatgtcagtggcgcacta--tataatttcatactcatttgctgtaatttatgttttagtttgctaattcctcctttca---taaacagCGTTTTGCTGCGGTTATCATGAGAATAAGAGAACCAAAAACTACAGCTCTGATATTTGCATCGGGTAAAATG
upper sequence: GLYMA09G41330.2 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os12g39070.1 (Oryza sativa), 3'ss of exon 2
ttttatctgagatcaataattaatttgcatgctagacatgtctttatgc-tgattggtcatttatctgcagtgcttatgtctatcttttgaatctttgcagCGTTTTGCTGCTGTTATTATGAGGATCAGGGAACCAAAAACTACTGCACTCATTTTTGCATCTGGCAAGATG
| ||||| | | || | | | || | || | | | | ||| || | || | || | | |||||||||||||| ||||| ||||| || || ||||| |||||||| || || || |||||||| || || |||
tgcacactgaggtta-tagcatctctatctactccatccgttccaaaatataagcactgtaatatatgttttagtttgctaactcctcttttcacaaacagCGTTTTGCTGCAGTTATCATGAGAATAAGAGAACCGAAAACTACAGCTCTGATATTTGCATCGGGTAAAATG
upper sequence: GLYMA09G41330.2 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os10g29660.2 (Oryza sativa), 3'ss of exon 2
----------------------------------ttttatctgagatcaataattaatttgcatgctagacatgtctttatgctg-attggtcat-ttatctgcagtgcttatgtctatcttttgaatctttgcagCGTTTTGCTGCTGTTATTATGAGGATCAGGGAACCAAAAACTACTGCACTCATTTTTGCATCTGGCAAGATG----------------------------
|| | || | | || | | || |||| | | | | ||| || | | | || | | || | |||| |||| |||||||||||||| ||||| |||||||| ||||| ||||| || || || || || ||||| || || ||||||
gtatagcttcagcttctgatgctttctattcagtttctttcaggaacaaaacacggaattacatgtcatgtctataatctaactgtatcatttgtgtcatgtctataatctaactgtatcatttgtgctcggacagCGTTTTGCTGCAGTTATCATGAGGATAAGGGACCCAAAGACAACAGCCCTGATATTTGCTTCGGGAAAGATGGTTTGCACTGGAGCAAAGAGCGAAGACC
upper sequence: GLYMA09G41330.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv06s0004g00180.t01 (Vitis vinifera), 3'ss of exon 3
ttttatctgagatcaataattaatttgcatgctagacatgtcttta---tgctgattggtcatttatctgcagtgcttatgtctatcttttga-atctttgcagCGTTTTGCTGCTGTTATTATGAGGATCAGGGAACCAAAAACTACTGCACTCATTTTTGCATCTGGCAAGATG
| ||| | | || || || || | ||| | | ||| || | | | ||| | | || ||| | |||||||||||||||| || || |||||||| ||||| |||||||| || || | || ||||| ||||| ||||||
----gatcaacatcttaaccttgttcctattggaggaattttttttctttccctatttgttgccagttttttttatgtattttaaatttatgatgttcctgcagCGTTTTGCTGCCGTAATCATGAGGATAAGGGACCCAAAAACCACGGCTTTGATATTTGCTTCTGGAAAGATG
upper sequence: GLYMA09G41330.2 (Glycine max), 3'ss of exon 3
lower sequence: PP1S246_34V6.1 (Physcomitrella patens), 3'ss of exon 2
ttttatctgagatcaataattaatttgcatgctagacatgtctttatgctgattggtcatttatctgcagtgcttatgtctatcttttgaatctttg----cagCGTTTTGCTGCTGTTATTATGAGGATCAGGGAACCAAAAACTACTGCACTCATTTTTGCATCTGGCAAGATG
|| | || | ||| | | || ||| ||| | || || | | | ||| || |||| | | | || | | ||| ||||||||||| |||||||||||| | || ||||| |||||||| ||||| ||||||||||||||||| || |||
--ttgaatatcgtcga-gtttactattgatactattcatttgttgatatttttggtgttgttacctatt-tgctcaacgccttgttgggcactattgtgtacagCGTTTTGCAGCTGTTATTATGCGAATAAGGGAGCCAAAAACGACTGCCCTCATTTTTGCATCTGGTAAAATG
upper sequence: GLYMA09G41330.2 (Glycine max), 3'ss of exon 3
lower sequence: PP1S13_321V6.1 (Physcomitrella patens), 3'ss of exon 2
--ttttatc-tgagatcaataattaatttgcatgctagac--atgtctttatgctgattggtcatttatctgcagtgcttatgtctatcttttgaatctttgcagCGTTTTGCTGCTGTTATTATGAGGATCAGGGAACCAAAAACTACTGCACTCATTTTTGCATCTGGCAAGATG
|| || ||| ||| || | || | || | || || | | | ||| | | | | | || ||| | | || ||||||||||| |||||||| ||| | |||||||| || ||||| ||||| || ||||||||||| || || |||
ctggttgtcatgaagacaacttgtactgtgtttctcaggctgatactgttgcttttgcttcttattcacccaatgcgttggtgggtattgt-----tgttcacagCGTTTTGCAGCTGTTATCATGCGAATCAGGGAGCCTAAAACAACTGCTCTTATTTTTGCATCCGGTAAAATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgctgattggtcatttatctgcagtgcttatgtctatcttttgaatctttgcagCGTTTTGCTGCTGTTATTATGAGGATCAGGGAACCAAAAACTACTGCACTCATTTTTGCATCTGGCAAGATG
tgctgat putative branch site (score: 3)
tctttgc putative PPT
tcatttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttttatctgagatcaataattaatttgcatgctagacatgtctttatgctgattggtcatttatctgcagtgcttatgtctatcttttgaatctttgcagCGTTTTGCTGCTGTTATTATGAGGATCAGGGAACCAAAAACTACTGCACTCATTTTTGCATCTGGCAAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG