Sequence
atgc intronic sequence ATGC exonic sequence...tgagcaatgagcattctcaactcatttaactgttcatcttcctttttgtgttttgtgttttatgatttctctttatttctaaagggtgtttgtgtatcagGCATAGGTGGACTGGGAGATATGAAGCTCATCTTTGGGACAACAGCTGCAAGAAAGAGGGGCAAAGCAGGAAAGGAAGACAAG
Basic information
species | Glycine max |
transcript | GLYMA05G22970.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G22970.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os03g56050.1 (Oryza sativa), 3'ss of exon 2
---tgagcaatgagcattct--caactcatttaactgttcatcttcctttttgtgttttgtgttttatgatttctctttatttc---taaagggtgtttgtgtat--cagGCATAGGTGGACTGGGAGATATGAAGCTCATCTTTGGGACAACAGCTGCAAGAAAGAGGGGCAAAGCAGGAAAGGAAGACAAG
||| | ||| | || | || || | | | | || || | ||| ||| | || |||| |||| | ||||||||||||||||||||||||||| || || || |||||||||||||||||||| || || || | ||| |||||| | ||||
gtagtagctagcagcgccatagtgacagacacctctcgccaccatgccgccatggcttccaccttcacagcttcacttaacctcaagtaaaaaaaccttgtaaaaagcagGCATAGGTGGACTGGGAGATATGAGGCACACCTCTGGGACAACAGCTGCAAGAAGGAAGGCCAGACCAGAAAAGGACGCCAAG
upper sequence: GLYMA05G22970.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os03g12950.1 (Oryza sativa), 3'ss of exon 2
tg-agcaatgagcattctcaactcatttaactgttcatcttcctttttgtgttttgtgttttatgatttctctttatttctaaagggtgtttgtgtatcagGCATAGGTGGACTGGGAGATATGAAGCTCATCTTTGGGACAACAGCTGCAAGAAAGAGGGGCAAAGCAGGAAAGGAAGACAAG
|| | ||||| || || | | || || | || |||| | || |||| ||| | | | | | | || | |||||| ||||||||||| ||||||||||| || || ||||| ||||| ||||| || || || || | ||||| ||||| ||||
tgtattgatgaggcacctactcttttgtttttgagcaaatcatttgaccctttttatattgaatgacgaaggtttgtgtgtgtttgat-tcactggagcagGCACAGGTGGACTGGAAGATATGAAGCCCACCTCTGGGATAACAGTTGCAAAAAGGATGGACAGACAAGGAAGGGAAGGCAAG
upper sequence: GLYMA05G22970.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G146688_T01 (Zea mays), 3'ss of exon 2
-------tgagcaatgagcattctcaactcatttaactg-ttcatcttcctttttgtgttttgtgtttta---tgatttctctttatttctaaag--ggtgtttgtgtatcagGCATAGGTGGACTGGGAGATATGAAGCTCATCTTTGGGACAACAGCTGCAAGAAAGAGGGGCAAAGCAGGAAAGGAAGACAAG
| || || | || | | || |||| | | || || | || | | | | | | || || ||||| | | | | ||||||||||||||| ||||| ||||| || || || |||||||||||||||||||| || || || |||||||| || | ||||
gtacgtacgtacacgccgccgtgtcgagctagttgactggtccgtccgcccgtccgtccatggagctgaagctgaagttgaaactaaaactaaaactgaaagtaattaagcagGCATAGGTGGACGGGGAGGTATGAGGCGCACCTGTGGGACAACAGCTGCAAGAAGGAAGGCCAGAGCAGGAAGGGCCGGCAAG
upper sequence: GLYMA05G22970.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G021573_T02 (Zea mays), 3'ss of exon 1
------tgagcaatgagcattctcaactcatttaactgttcatcttcctttttgtgttttgtgttttatgatttctctttatttctaaagggtgtttgtgtatcagGCATAGGTGGACTGGGAGATATGAAGCTCATCTTTGGGACAACAGCTGCAAGAAAGAGGGGCAAAGCAGGAAAGGAAGACAAG
| || | || | ||| || ||| | | | |||| | | || | | | ||| | ||| | | | || | || | |||||| ||||||||||||||||| ||||| || || |||||||||||||||| ||| || ||||| | || ||||| |||||||
tgtctgttagggccaaacagttcagactgtttgaaccg-----cgactgttttatactgaatgatggagggttt-tgtttgtgttggattggattcactggagcagGCACAGGTGGACTGGGAGATACGAAGCCCACCTCTGGGACAACAGCTGCAGGAAGGATGGGCAGACTAGAAAAGGCAGACAAG
upper sequence: GLYMA05G22970.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G021573_T01 (Zea mays), 3'ss of exon 2
---------tgagcaatgagcattctcaactcatttaactgttcatcttcctttttgtgttttgtgttttatgatttctctttatttctaaagggtgtttgtgtatcagGCATAGGTGGACTGGGAGATATGAAGCTCATCTTTGGGACAACAGCTGCAAGAAAGAGGGGCAAAGCAGGAAAGGAAGACAAG
| || | || | ||| || ||| | | | |||| | | || | | | ||| | ||| | | | || | || | |||||| ||||||||||||||||| ||||| || || |||||||||||||||| ||| || ||||| | || ||||| |||||||
ctctgtctgttagggccaaacagttcagactgtttgaaccg-----cgactgttttatactgaatgatggagggttt-tgtttgtgttggattggattcactggagCAGGCACAGGTGGACTGGGAGATACGAAGCCCACCTCTGGGACAACAGCTGCAGGAAGGATGGGCAGACTAGAAAAGGCAGACAAG
upper sequence: GLYMA05G22970.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G028151_T01 (Zea mays), 3'ss of exon 2
---------tgagcaatgagcattctcaactcat-----ttaactgttcatcttcctttttgtgttttgtgttt-tatgatt---tctctttatttctaaagggtgttt----gtgt---atcagGCATAGGTGGACTGGGAGATATGAAGCTCATCTTTGGGACAACAGCTGCAAGAAAGAGGGGCAAAGCAGGAAAGGAAGACAAG
| || | | | | | | | | | | | | | | | ||| || || | | ||| | ||| | ||||||||||||||| ||||| ||||| || || || |||||||||||||||| ||| || ||||| | | ||||||| | ||||
gtatcctcccaactcccgaccgtccgtacgccgtcgctgtcgcaggcgcgcgcgacccgcagcatccggcgcccgtgcgatcgagtcgctcactggccgcgtggtttcccaccgtgcaaaagcagGCATAGGTGGACGGGGAGGTATGAGGCGCACCTCTGGGACAACAGCTGCAGGAAGGAAGGGCAGACCCGGAAAGGCCGGCAAG
upper sequence: GLYMA05G22970.1 (Glycine max), 3'ss of exon 4
lower sequence: AT4G37750.1 (Arabidopsis thaliana), 3'ss of exon 2
tgagcaatgagcattctcaactcatttaactgttcatcttcctttttgtgttttgtgttttatgatttctctttatttctaaagggtgtttgtgtatcagGCATAGGTGGACTGGGAGATATGAAGCTCATCTTTGGGACAACAGCTGCAAGAAAGAGGGGCAAAGCAGGAAAGGAAGACAAG
|| | | |||| | | | |||| ||| || | ||| | | | | |||| ||| | |||| | ||| ||||| |||||||| ||||||||||||||||| |||||||| || | |||||| || || || || || |||||||||||||
------------gttgtttttttattttataatattaaactttgtttgactttcgttagtaatgttacatatacttacttaaaaggt-tatgtgaaacagACATAGATGGACTGGTAGATATGAAGCTCATCTATGGGACAATAGTTTCAAGAAGGAAGGTCACAGTAGAAAAGGAAGACAAG
upper sequence: GLYMA05G22970.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv07s0151g00440.t01 (Vitis vinifera), 3'ss of exon 2
tgagcaatgagcattctcaactcat---ttaactgttcatcttcctttttgtgtt-ttgtgt-tttatgatttctctttatttctaaagggtgttt---gtgtatcagGCATAGGTGGACTGGGAGATATGAAGCTCATCTTTGGGACAACAGCTGCAAGAAAGAGGGGCAAAGCAGGAAAGGAAGACAAG
| | || | ||||| | | || ||||||| || | | | | |||| | | | ||| ||||| ||||| || |||||||||||| ||||| || ||||||||||||||||| ||||||||||| ||||||||||| |||||||||||||||||||| ||||
--------gtgtttttttccctcatgtttcccccttttgccttccttgttttcctatcacatctttaccttctttttttttttctttttcctgttttatgtctatcagGCATAGATGGACAGGTAGATATGAAGCTCATCTATGGGACAACAGTTGCAAGAAAGAAGGGCAAAGCAGGAAAGGAAGGCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgtgttttgtgttttatgatttctctttatttctaaagggtgtttgtgtatcagGCATAGGTGGACTGGGAGATATGAAGCTCATCTTTGGGACAACAGCTGCAAGAAAGAGGGGCAAAGCAGGAAAGGAAGACAAG
ttctaaa putative branch site (score: 2)
ttttatgatttctctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgagcaatgagcattctcaactcatttaactgttcatcttcctttttgtgttttgtgttttatgatttctctttatttctaaagggtgtttgtgtatcagGCATAGGTGGACTGGGAGATATGAAGCTCATCTTTGGGACAACAGCTGCAAGAAAGAGGGGCAAAGCAGGAAAGGAAGACAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- agcaatg
- - - - - gcattct
- - - - - - - - -caactca
- - - - - - - - - - - - - - - - - catcttc
- - - - - - - - - - - - - - - - - - - - - - - - tgttttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gggtgtt