Sequence
atgc intronic sequence ATGC exonic sequencegtgagtttcatccattgttcctcaggaataaaatgaaaaaaaatatataatttatacaataattaacaataaaccattttaactatttgcctttttttgatagGTGGCATTCTTCAGGCAATTTTTCGGGTCTGTCACTAAGGTGGATTACATGACCATGCGGCACGGATTTATTAAC
Basic information
species | Glycine max |
transcript | GLYMA04G01730.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G01730.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os03g03700.2 (Oryza sativa), 3'ss of exon 6
gtgagttt---catcca-ttgttcctcaggaataaaatgaaaaaaaata------tataatttata-caataattaacaataaaccattttaactatttgcctttttttgatagGTGGCATTCTTCAGGCAATTTTTCGGGTCTGTCACTAAGGTGGATTACATGACCATGCGGCACGGATTTATTAAC
||||||| || | | | | || | ||| | || ||| || || | | ||| |||| | ||||| ||| ||| |||||||| ||||||||||| || |||||||||||||| |||||||| ||| ||||||||||||| || || || ||
gtgagttcttgcacctaatcgatctctacctgcctaatctttgcagctacctggttattgttcgtatccaacattttttttaaagaaaaaaaactacca--tgtttgttgttagGTGGCGTTCTTCAGGCAGTTCTTCGGGTCTGTCACCAAGGTGGACTACCTGACCATGCGGCAAGGCTTCATCAAT
upper sequence: GLYMA04G01730.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os06g29110.1 (Oryza sativa), 3'ss of exon 6
-------gtgagtttc---atccat---tgttcctcaggaataaaatgaaaaaaaatatat-aatttatacaataattaacaataaaccattttaactatttgcctttttttgatagGTGGCATTCTTCAGGCAATTTTTCGGGTCTGTCACTAAGGTGGATTACATGACCATGCGGCACGGATTTATTAAC
| | | || || ||| |||| | | | || | | | |||| | | ||| || | ||| | | | || ||| ||| ||||| |||||||||||||| || || ||||| ||||| |||||||| ||| ||||||||||||| || || || ||
gtgagttatcaatctccgaatacatgcttgttttttattcttgcaactggcctagctgttccaattcaatccatattttttgaaaaaaaaaat-attcatgccgtgtttgttgttagGTAGCATTCTTCAGGCAGTTCTTTGGGTCCGTCACCAAGGTGGACTACCTGACCATGCGGCAAGGCTTCATCAAT
upper sequence: GLYMA04G01730.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G032219_T02 (Zea mays), 3'ss of exon 6
gtgagtttcatccattgttcctcaggaata---aaatgaaaaaaaatatataatttat--acaataattaacaa--taaaccattttaactatttgcctttttttg------atagGTGGCATTCTTCAGGCAATTTTTCGGGTCTGTCACTAAGGTGGATTACATGACCATGCGGCACGGATTTATTAAC
|||||| | | | || ||| | | | | | ||| | | || | | || | | | ||| | ||| | ||||||| ||||||||||| || |||| ||| || || |||||||||||| ||||||||||||| || || || |||
gtgagtact-ccgacggatcgccagctctttgcagcctgttcctatcgttaagtttctccgcctcgttttatagcctaggctctctgaacactccccctcccccggcccgctgcagGTGGCGTTCTTCAGGCAGTTCTTCGCGTCCGTGACCAAGGTGGATTACCTGACCATGCGGCAGGGGTTCATCAAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatttatacaataattaacaataaaccattttaactatttgcctttttttgatagGTGGCATTCTTCAGGCAATTTTTCGGGTCTGTCACTAAGGTGGATTACATGACCATGCGGCACGGATTTATTAAC
ttttaac putative branch site (score: 2)
ctatttgccttttttt CT-rich tract
atacaataattaacaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtttcatccattgttcctcaggaataaaatgaaaaaaaatatataatttatacaataattaacaataaaccattttaactatttgcctttttttgatagGTGGCATTCTTCAGGCAATTTTTCGGGTCTGTCACTAAGGTGGATTACATGACCATGCGGCACGGATTTATTAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA