Sequence
atgc intronic sequence ATGC exonic sequencegtctgttgacttttgctaatggtatccttaaattgtttgcaaaagaaggtctgttgtgacatgggtcctttatttttttctgattatggaatatttatttcccttttatctttctgtagGCTCCTTGTATAATTTTTATTGATGAAATTGATGCTGTTGGATCAACAAGAAAACAATGGGAGGGCCACACAAAGAAGACATTGCATCAGCTACTTGTTG
Basic information
species | Glycine max |
transcript | GLYMA13G08160.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G08160.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os01g43150.1 (Oryza sativa), 3'ss of exon 9
gtctgttgacttttgctaatggtatccttaaattgtttgcaaaagaaggtctgttgtgacatgggt--cctttatttttttctgattatggaatatt-----------tatttcccttttatctttctgtagGCTCCTTGTATAATTTTTATTGATGAAATTGATGCTGTTGGATCAACAAGAAAACAATGGGAGGGCCACACAAAGAAGACATTGCATCAGCTACTTGTTG
| ||| || || | | || |||| | || | | | | || | | || |||| ||| ||| | | | || ||| ||| || | | |||| || || || |||| ||||||||||| |||||||| || ||||| |||||||| ||||| || ||||||||||| ||||||||||| || ||||| |
--gttctgatttctg--agccctttctctaaac-atgtgttgctctgagcttaatctcacccagtttgcccttatgatttctagatcgtagtgtgttgccttgttaaacattcatagtttccctctttacagGCGCCATGCATTGTTTTCATTGATGAAATAGATGCTGTGGGTTCAACTAGAAAACAGTGGGAAGGACACACAAAGAAAACATTGCATCAACTTCTTGTCG
upper sequence: GLYMA13G08160.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G004040_T01 (Zea mays), 3'ss of exon 9
gtctgttgacttttgctaatggtatccttaaattgtttgcaaaagaaggtctg-ttgtgacatgggtcctttatttttttctgattatggaatatttatttcccttttatctttctgtagGCTCCTTGTATAATTTTTATTGATGAAATTGATGCTGTTGGATCAACAAGAAAACAATGGGAGGGCCACACAAAGAAGACATTGCATCAGCTACTTGTTG
|| || | | || | || || | || | | ||| || | ||| | | | || | | |||||| |||| |||| || || || |||| ||||||||||| |||||||| |||||||| || ||||| ||||| || ||||||||||||||||||||||| || |||||||
----------agttatatattggaaactgatatcgtccaaagaatcttatatacttgaagagaggagaatgccgctttagccagcttt--aacaatcatttcctctttac--------agGCACCATGCATTGTTTTCATTGATGAAATAGATGCTGTGGGATCAACTAGGAAACAGTGGGAAGGGCACACAAAGAAGACATTGCATCAACTTCTTGTTG
upper sequence: GLYMA13G08160.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G156069_T01 (Zea mays), 3'ss of exon 9
gtctgttgacttttgctaatggtatccttaaattgtttgcaaaagaaggtctgttg-tgacatgggtcctttatttttttctgattatggaatatttatttcccttttatctttctgtagGCTCCTTGTATAATTTTTATTGATGAAATTGATGCTGTTGGATCAACAAGAAAACAATGGGAGGGCCACACAAAGAAGACATTGCATCAGCTACTTGTTG
| ||| | ||| || |||| |||| | | | || |||| | || | | | | | | ||||| | || | | | ||| | | |||| || || || | || ||||||||||| |||||||| || ||||| |||||||| ||||| || |||||||||||||| |||||||| || |||||||
--------------gataa-gttattctgaaat-----gcaatattttatgttttactgacttaataccatgaaaactaaaggtcaaagtaatatattttaacaatctttctctttacagGCGCCATGCATTGTCTTCATTGATGAAATAGATGCTGTGGGTTCAACTAGAAAACAGTGGGAAGGGCACACAAAGAAGACGTTGCATCAACTTCTTGTTG
upper sequence: GLYMA13G08160.1 (Glycine max), 3'ss of exon 9
lower sequence: AT5G53170.1 (Arabidopsis thaliana), 3'ss of exon 9
gtctgttgacttttgctaatggtatccttaaattgtttgcaaaagaaggtctgttgtgacatgggtccttt-atttttttctgattatggaatatttatttccctt--ttatctttc--tgtagGCTCCTTGTATAATTTTTATTGATGAAATTGATGCTGTTGGATCAACAAGAAAACAATGGGAGGGCCACACAAAGAAGACATTGCATCAGCTACTTGTTG
|||| | || | | | | || || | | | | | || ||| | || | ||| ||||| | | ||| | | |||| |||||||| ||||| ||||| |||||||||||||||||||| ||||||||||||||||| || || |||||||||||||||||||| ||||||||||
---------------------gtatgactcaacttgtcactgcttatcagctattttaaaagagtttggttgattaggctaccatgaatgaacttttatatttaatgacgatcatgtgttacagGCACCTTGTATTATTTTCATTGACGAAATTGATGCTGTTGGATCCACAAGAAAACAATGGGAAGGGCATACAAAGAAGACATTGCATCAACTACTTGTTG
upper sequence: GLYMA13G08160.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv16s0050g02630.t01 (Vitis vinifera), 3'ss of exon 9
gtctgttgacttttgctaatggtatccttaaattgtttgcaaaagaaggtctgttgtgacatgggtcctttatttttttctgattatggaatatttatttcccttttatctttctgtagGCTCCTTGTATAATTTTTATTGATGAAATTGATGCTGTTGGATCAACAAGAAAACAATGGGAGGGCCACACAAAGAAGACATTGCATCAGCTACTTGTTG
| ||| || | || | | || || || || |||| | | | | ||| | | |||| || |||| | |||| ||||||||||| || ||||| ||||||||||| |||||||||||||| ||| |||| |||||||| ||||| ||||| || |||||||| || || |||||||
--------------ctttatgtagatttttacttatgtacatgg---tgttaattcggatatggaat-tggagatccattaaattttagctcattttttgtactttcttatttc-atagGCTCCTTGCATCATTTTCATTGATGAAATAGATGCTGTTGGATCTACACGAAAGCAATGGGAAGGCCATACAAAAAAAACATTGCACCAACTGCTTGTTG
upper sequence: GLYMA13G08160.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S9_238V6.1 (Physcomitrella patens), 3'ss of exon 9
-----------------------gtctgttgacttttgctaatggtatccttaaattgtttgcaaaagaaggtctgt---tgtgacatg--ggtcctttatttttttctgattatggaatatttatttcccttttatctttctgtagGCTCCTTGTATAATTTTTATTGATGAAATTGATGCTGTTGGATCAACAAGAAAACAATGGGAGGGCCACACAAAGAAGACATTGCATCAGCTACTTGTTG
||| | | || | | || ||| || || | |||| | ||| || ||| | | | || || | || ||| ||| | | |||||||||| || | |||||||||||||||||||||||||| | | || |||||||| ||||| || || || || || ||||| | || || |
gtacatttcgtataaaccaatacccttgtataatattctcttttacactctcgtattcattcttcaaaagaatctgcatatatgatttgctggttttacagagaacttcagttctgtggttttgattgattgtttgtg--gcgacagGCTCCTTGCATCGTCTTTATTGATGAAATTGATGCTGTTGGGGGCAGCCGCAAGCAATGGGAAGGCCATACGAAAAAAACTCTGAATCAGTTGCTGGTAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtcctttatttttttctgattatggaatatttatttcccttttatctttctgtagGCTCCTTGTATAATTTTTATTGATGAAATTGATGCTGTTGGATCAACAAGAAAACAATGGGAGGGCCACACAAAGAAGACATTGCATCAGCTACTTGTTG
ttctgat putative branch site (score: 3)
tatttatttccctttt putative PPT
ttatttttttctgatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtctgttgacttttgctaatggtatccttaaattgtttgcaaaagaaggtctgttgtgacatgggtcctttatttttttctgattatggaatatttatttcccttttatctttctgtagGCTCCTTGTATAATTTTTATTGATGAAATTGATGCTGTTGGATCAACAAGAAAACAATGGGAGGGCCACACAAAGAAGACATTGCATCAGCTACTTGTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT