Sequence
atgc intronic sequence ATGC exonic sequencegtatgtttgattttcattattgtgtctttcactatttcttttcctatggattccaatttattttctcattagctagcaatcaaaatttgaatactcgtgcagATGGGGCTCATGAAGAAACATCCTTCAATTATACCATTCATGATACACATTACAAATGAGGATAAGCACTTGGAAAGATTTGCTGTACGTGCGAAGTATA
Basic information
species | Glycine max |
transcript | GLYMA12G08340.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G08340.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os02g57400.2 (Oryza sativa), 3'ss of exon 4
gtatgtttgattttcattattgtgtctttcactatttcttttcctatggattccaatttattttctcattagctagcaatcaaaatttgaatactcgtgcagATGGGGCTCATGAAGAAACATCCTTCAATTATACCATTCATGATACACATTACAAATGAGGATAAGCACTTGGAAAGATTTGCTGTACGTGCGAAGTATA
|| ||| | | ||| | | | | ||| ||| | || || || || || | |||| | |||| || || ||||||||||| ||||||||||| ||||| || |||||||| ||| || ||||| | |||||||| || ||| |||| |||| ||||||||||| ||||| |
gtgcgttgcgtactagttag-atatttgcatcaattacttatactttg--ttgcatactagagaactgatg--tagccttttctattttcattttccaacagATGGGGCTAATGAAGAAACACCCTTCCATAATACCATTTATGGTATACATTGCGAATGAGGAGAAACACATGGAGCGATTCGCTGTACGTGCAAAGTACA
upper sequence: GLYMA12G08340.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G342327_T01 (Zea mays), 3'ss of exon 4
-----------------------------gtatgtttgattttcatta-ttgtgtctttcactatttcttttcctatggattccaatttattttctcattagctagcaatcaaaa-----tttgaatactcgt--gcagATGGGGCTCATGAAGAAACATCCTTCAATTATACCATTCATGATACACATTACAAATGAGGATAAGCACTTGGAAAGATTTGCTGTACGTGCGAAGTATA
|| | |||| | | |||| | || | | | || ||| | | || | |||||| | ||| | || ||| || | | | |||||||| | ||||||||||||||||| || |||||||| ||| || ||||||||||||||||||| ||| ||||| |||||||||||||||| ||||| |
gtacgtattagtcaagaaacagtgcaggggtgaggggtatttcaaaaaattgtttagtttatgttgttttccgttatttagttatatctcatttctcgt-agccactgattaaagtcttcttctgctgttaatcaacagATGGGATTAATGAAGAAACATCCTTCCATAATACCATTTATGGTATACATTACAAATGAGGATAAACACATGGAACGATTTGCTGTACGTGCAAAGTACA
upper sequence: GLYMA12G08340.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G123544_T01 (Zea mays), 3'ss of exon 4
gtatgtttgattttcattattgtgtctttcactatttctttt-cctatggattccaatttattttctcattagctagcaatcaaaatttg--aatactcgtg--------cagATGGGGCTCATGAAGAAACATCCTTCAATTATACCATTCATGATACACATTACAAATGAGGATAAGCACTTGGAAAGATTTGCTGTACGTGCGAAGTATA
||| || | | | | | | | | | || ||| |||||| || ||| |||| | || | ||| | | || | | | || || |||||||| | |||||||| |||||||| || |||||||||||| || |||| ||||| ||||| || ||| ||||| | |||||||| ||||||||||| |
gtacgtatcagtca-agaaacgaaaatgagattgttcgtttagcctatgcttttttttttttttttttgc-agatggcactgactatacgctacttctactgttgaccgacagATGGGATTAATGAAGAAGCATCCTTCCATAATACCATTCATGGTATACATCACAAACGAGGAGAAACACATGGAACGGTTTGCTGTGCGTGCGAAGTACA
upper sequence: GLYMA12G08340.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G017334_T01 (Zea mays), 3'ss of exon 4
--------------------------------------------------------------------gtatgtttgattttcattattgtgt--ctttcactatt---tcttttcctatggattccaa--tttattttctcattagctag--caatcaaaatttgaat---actcgtgcagATGGGGCTCATGAAGAAACATCCTTCAATTATACCATTCATGATACACATTACAAATGAGGATAAGCACTTGGAAAGATTTGCTGTACGTGCGAAGTATA
| | || | ||||| | ||| ||| | | | | || || || ||| | || | | | || | |||| | | | | |||||||| || |||| |||||||||||| || ||||| |||||||| |||| | ||||||| ||||||| || || |||||||||||||| ||||| |
gtatgtgcttccagaaaactattcatttgcatttctttcctatcattccagctattgattcttttaggtcgtatcagacccactatattgcatttcttctgctaatagaagtggagttgttagttgtaacattcattgttaacttgcccaaattattctacatttccttttaattattccagATGGGTCTAATGAGGAAACATCCTTCGATCATACCTTTCATGATCTACATCTCTAATGAGGGTAAGCACACAGAGAGGTTTGCTGTACGTGCAAAGTACA
upper sequence: GLYMA12G08340.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G048553_T02 (Zea mays), 3'ss of exon 4
gtatgtttgattttcattattgtgtctttcactatttcttttcctatggattcca--atttattttctcattagctagca-atcaaaatttgaatactcgtgcagATGGGGCTCATGAAGAAACATCCTTCAATTATACCATTCATGATACACATTACAAATGAGGATAAGCACTTGGAAAGATTTGCTGTACGTGCGAAGTATA
| | | ||| | | | || | | | || || |||| | | || | | || || ||| | || | |||||||| || |||| |||||||||||| || ||||| |||||||| |||| | |||||| ||||||| || || |||||||||||||||||||| |
--agagccactatattgcatttgttttgctaataaaggtggagttgtaactttcattgtttacatgcccactttattccacatttcgttttaattattt---cagATGGGTCTAATGAGGAAACATCCTTCGATAATACCTTTCATGATCTACATATCTAATGAGAGTAAGCACACAGAGAGGTTTGCTGTACGTGCGAAGTACA
upper sequence: GLYMA12G08340.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv06s0061g00280.t01 (Vitis vinifera), 3'ss of exon 5
gtatgtttgattttcattattgtgtctttcactatttcttttcctatggattccaatt-tattttctcattagctagcaatcaaaatttgaatactcgtgcagATGGGGCTCATGAAGAAACATCCTTCAATTATACCATTCATGATACACATTACAAATGAGGATAAGCACTTGGAAAGATTTGCTGTACGTGCGAAGTATA
||| || | | | | | | ||| | |||| | | ||| || | | |||| | |||| || |||| || ||| |||||||||||| |||||||||||||| ||||| ||||||||||||||| |||| |||||||| || || ||||||||| |||||||||| ||||| |||||||
gtaagtgtcttcactaattctaattttttttttccttctcctgacaaggaatcttttagtgttttgtttttagtta-caatggttgttccaattg----gcagATGGGGCTTATGAAGAAACATCCGTCAATCATACCATTCATGATATACATCACAAATGAAGACAAACACTTGGAACGATTTGCTGTTCGTGCAAAGTATA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggattccaatttattttctcattagctagcaatcaaaatttgaatactcgtgcagATGGGGCTCATGAAGAAACATCCTTCAATTATACCATTCATGATACACATTACAAATGAGGATAAGCACTTGGAAAGATTTGCTGTACGTGCGAAGTATA
aatttattttctcatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtttgattttcattattgtgtctttcactatttcttttcctatggattccaatttattttctcattagctagcaatcaaaatttgaatactcgtgcagATGGGGCTCATGAAGAAACATCCTTCAATTATACCATTCATGATACACATTACAAATGAGGATAAGCACTTGGAAAGATTTGCTGTACGTGCGAAGTATA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT