Sequence
atgc intronic sequence ATGC exonic sequencegtagttggcatttttaacttgttttataattatttactttttcagACTGCTGCAAGCTATCATGCAATAGCTATTGCTCTTTCTTTGATGGAAGCATACTCTCTAAGTGTTCAGCATGAACAGACCACCCTCCAAATCCTGCAGG
Basic information
species | Glycine max |
transcript | GLYMA04G24430.1 |
intron # | 19 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G24430.1 (Glycine max), 3'ss of exon 19
lower sequence: LOC_Os02g15660.1 (Oryza sativa), 3'ss of exon 2
-----------------------------------------------------------------------------------------------------------------------------------------gtagttggcatttttaacttgttttataattatttacttttt------cagACTGCTGCAAGCTATCATGCAATAGCTATTGCTCTTTCTTTGATGGAAGCATACTCTCTAAGTGTTCAGCATGAACAGACCACCCTCCAAATCCTGCAGG
| ||| | | |||| | ||||| | || | |||| ||||||||||| || || ||||| || ||||||||||| ||||| ||||||||||||||| ||||||| || |||||| | ||||| | | ||| || || |
gtttgcaaccctatctgttttagttctcaattgagttccgacacatacagtagtctaattcatggccacatcagttttgatgttcacactcgttttgctgggaactatgagaaccattccctttcatgatccaaagaaaacttgagactgaaaactcatcttatatatcttgatgtttttattgacagACTGCTGCTAGTTACCATGCTATTGCTATTGCTCTGTCTTTAATGGAAGCATACTCTTTAAGTGTCCAACATGAAAAAACCACTTTACGAATACTTCAAG
upper sequence: GLYMA04G24430.1 (Glycine max), 3'ss of exon 19
lower sequence: AT4G28080.1 (Arabidopsis thaliana), 3'ss of exon 19
--------------------------------------------------gtagttggcatttttaact-----tgttttataattatttactttttcagACTGCTGCAAGCTATCATGCAATAGCTATTGCTCTTTCTTTGATGGAAGCATACTCTCTAAGTGTTCAGCATGAACAGACCACCCTCCAAATCCTGCAGG
|| || | | || | || |||| | ||||||||||||||||||||| ||||| || ||||||||||||||| ||||||| |||||||| | || ||||| ||||| |||||||| || || || || || |
ttcccattctatgaaggcttaggcttaataagtaaaatttaccatggaagctaaatgatacgctaaaacatgaattcactactgttatgtttcttttcagACTGCTGCAAGCTACCATGCCATTGCTATTGCTCTTTCTCTGATGGACGCATACTCCTTGAGCGTTCAACATGAGCAGACCACTCTACAGATTCTACAAG
upper sequence: GLYMA04G24430.1 (Glycine max), 3'ss of exon 19
lower sequence: Vv11s0037g00840.t01 (Vitis vinifera), 3'ss of exon 19
----gtagttggcatttttaacttgttttataattatttactttttcagAC--TGCTGCAAGCTAT---CATGCAATAGCTATTGCTCTTTCTTTGATGGAAGCATACTCTCTAAGTGTTCAGCATGAACAGACCACCCTCCAAATCCTGCAGG
| || || |||| | || | || ||||| ||| | | | | | | |||| | | || ||| |||| || | | ||| | | || | |
cttggaagctgattttttgggttgtttgtgcaaatatttgggacactagatgttattcctggttctgaacatgtttaacccatgcttctgtcttcttcagACTGCTGCCAGCTATCATGCTATAGCAATTGCACTGTCTTTG------------
upper sequence: GLYMA04G24430.1 (Glycine max), 3'ss of exon 19
lower sequence: PP1S363_15V6.1 (Physcomitrella patens), 3'ss of exon 15
-------------------------------------------------------------------------------------------------------gtagttggcattttta--acttgttttataattatttactttttcagACTGCTGCAAGCTATCATGCAATAGCTATTGCTCTTTCTTTGATGGAAGCATACTCTCTAAGTGTTCAGCATGAACAGACCACCCTCCAAATCCTGCAGG
| || ||| ||| | | ||| | ||||| || || | ||||||||||| || ||||| || || || ||||| ||||| ||||||| || ||||| || ||||| ||||||||||| |||||| | || || | || |
gtttattccgaccctcaattctgctgggacactaattacttccagctgtgacgtcgtgaatgacggtgtaaccattagagctgtaatcgctgcagttttttattttattattattattattattattttcaaaattactt-tttctgcagACTGCTGCGAGTTATCACGCTATCGCAATTGCGCTTTCCCTGATGGAGGCGTACTCCCTCAGTGTCCAGCATGAACAAACCACCTTACAGATTTTACAAG
upper sequence: GLYMA04G24430.1 (Glycine max), 3'ss of exon 19
lower sequence: PP1S73_28V6.1 (Physcomitrella patens), 3'ss of exon 14
------------------------------------------------------------gtagt-tggcatttttaacttgttttataattatttactttttcagACTGCTGCAAGCTATCATGCAATAGCTATTGCTCTTTCTTTGATGGAAGCATACTCTCTAAGTGTTCAGCATGAACAGACCACCCTCCAAATCCTGCAGG
|| | || | || || | | | || || || || |||||||||||||| || || ||||| || ||||| ||||| | ||||| || ||||| || |||||||||||||| || || ||| | || || ||||
gttcgttgtaacactagttgttgaatttttttcgagtacaagtcgtttcatctttaacacttaccctatcactgcaaatttactaattgagtactt-ctgttgcagACTGCTGCAAGTTACCACGCAATTGCAATTGCGCTTTCACTTATGGAGGCTTACTCCCTCAGTGTTCAGCATGAGCAAACTACCTTACAGATTTTGCAAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtagttggcatttttaacttgttttataattatttactttttcagACTGCTGCAAGCTATCATGCAATAGCTATTGCTCTTTCTTTGATGGAAGCATACTCTCTAAGTGTTCAGCATGAACAGACCACCCTCCAAATCCTGCAGG
ttttaac putative branch site (score: 2)
ttatttactttttc putative PPT
atttttaacttgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagttggcatttttaacttgttttataattatttactttttcagACTGCTGCAAGCTATCATGCAATAGCTATTGCTCTTTCTTTGATGGAAGCATACTCTCTAAGTGTTCAGCATGAACAGACCACCCTCCAAATCCTGCAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG