Sequence
atgc intronic sequence ATGC exonic sequence...ataaatagataagctgtgttttatctattttatctaaaatatacaagcagatagatttgtcagaatcattagtctaacaaaaatttgcgtgtttgggaagATTCGTGATACGAGTGTTCTTGTGAGGTTGAGACCTGCATGGGAAGATCTTCGGAGCTACTTGACTGCAAGAGGGCGCAAGCGTTTTGAGGTTTATGTCT
Basic information
species | Glycine max |
transcript | GLYMA07G31430.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G31430.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os04g44710.2 (Oryza sativa), 3'ss of exon 3
ataaatagataagctgtgttttatctattttatctaaaatatacaagca-gatagatttgtcagaatcatta----gtctaacaaaaatttgcgtgtt--tgggaagATTCGTGATACGAGTGTTCTTGTGAGGTTGAGACCTGCATGGGAAGATCTTCGGAGCTACTTGACTGCAAGAGGGCGCAAGCGTTTTGAGGTTTATGTCT
| | ||||| | | |||||| | | ||||| || | | || | || ||| | ||| | || | | || | |||| | ||||| |||||||| || ||||||| ||||||||||| ||||||||||||||||| | ||||||||| ||||| ||||||||||| ||||| |
---gagcgctaagcact-tcccgtctattcagctttga---tacaaccatgttccatgtttccatgctgttatactgcctagttgattttccctttttcttaattagATAAGAGATACCAGTGTTCTGGTACGGTTGAGGCCTGCATGGGAGGATCTTCGGAGCTACTTAATTGCAAGAGGTCGCAAACGTTTTGAGGTATATGTGT
upper sequence: GLYMA07G31430.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os02g42600.1 (Oryza sativa), 3'ss of exon 2
ataaatagataagctgtgttttatctattttatctaaaata--tacaagcagatagatttgt-cagaatcattagtctaacaaaaatttgcgtgtt---tgggaagATTCGTGATACGAGTGTTCTTGTGAGGTTGAGACCTGCATGGGAAGATCTTCGGAGCTACTTGACTGCAAGAGGGCGCAAGCGTTTTGAGGTTTATGTCT
|| | | || ||| || | | | ||| ||||| || || || |||| ||| | || || | |||| | ||||| ||||||||||| | || || || |||||||| ||||| ||||||||||||| ||| ||||| ||||| ||||||||||| ||||| |
------cagcgtgccttttcacattgctttgatgtggcctgactttggttgcataagtttgtacaaaacttccaggctaaggctttttttttttttttttgtgtagATAAGGGATACCAGTGTTCTTGTACGTTTAAGGCCAGCATGGGAGGATCTCCGGAGCTACTTGATTGCTAGAGGTCGCAAACGTTTTGAGGTCTATGTGT
upper sequence: GLYMA07G31430.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G120373_T01 (Zea mays), 3'ss of exon 2
------ataaatagataagctgtgttttatctattttatctaaaatatacaagcagatagatttgtcagaatcattagtctaacaaaaatttgcgtgtttgggaagATTCGTGATACGAGTGTTCTTGTGAGGTTGAGACCTGCATGGGAAGATCTTCGGAGCTACTTGACTGCAAGAGGGCGCAAGCGTTTTGAGGTTTATGTCT
| | | || || | || ||| | || | ||| | | ||| |||| |||| ||| | | ||| ||| | ||||| | ||||| ||||| ||||| | || || || || ||||| |||||||| |||||||| | ||| ||||| ||||||||||||||||| ||||| |
gattctttgttgttgcatgtagttttcaaccttgtttggatctgattttgttgcacaaaaatt-gtca--atcagctatctgattttgttctgc---tttctgcagATTAGGGATACCAGTGTGCTTGTATGTTTAAGGCCAGCCTGGGAGGATCTTCGCAGCTACTTAATTGCCAGAGGTCGCAAGCGTTTTGAGGTCTATGTGT
upper sequence: GLYMA07G31430.1 (Glycine max), 3'ss of exon 2
lower sequence: AT4G21670.1 (Arabidopsis thaliana), 3'ss of exon 2
ataaatagataagctgtgttttatctattttatctaaaatatacaagcagatagatttgtcagaatcatta--gtctaacaaaaatttgcgtgtttgggaa--gATTCGTGATACGAGTGTTCTTGTGAGGTTGAGACCTGCATGGGAAGATCTTCGGAGCTACTTGACTGCAAGAGGGCGCAAGCGTTTTGAGGTTTATGTCT
| | | | | | || | |||| || | |||| ||||||| || |||| || | || ||| | ||| | |||||||||||| |||||||||||||| |||| || ||||||| || ||||| ||||| ||||| |||| |||||| ||||||||||| || ||||| |
-cttgtggtataaccttttatttttcatttgctcctttctg---gagcacctagatttttctgaattcttgtggctgaatctgcattcctatatttacacacagATTCGTGATACAAGTGTTCTTGTGAGAATGAGGCCCTCATGGGAGGAACTTCGAAGCTATTTGACAGCAAAAGGGCGTAAGCGTTTTGAAGTATATGTTT
upper sequence: GLYMA07G31430.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv00s0370g00040.t01 (Vitis vinifera), 3'ss of exon 2
ataaatagataagctgtgttttatctattttatctaaaa----tatacaagcagatagatttgtcagaatcattagtctaacaaaaatttgc-gtgtttgggaagATTCGTGATACGAGTGTTCTTGTGAGGTTGAGACCTGCATGGGAAGATCTTCGGAGCTACTTGACTGCAAGAGGGCGCAAGCGTTTTGAGGTTTATGTCT
| | || || | || | ||| | ||| || | | || | || | | | ||||| |||||| ||| | | | ||||||||||||| ||||| ||||||||| | |||||||||||||| || || ||||||||| | |||||||| |||||||||||||||||||||||||| |
--ataccactatact---tcttgtttatgtcatccaataagcctgtaaactcattccaagaaactggtttgtttagtgacacaaaatttttttatatctccacagATTCGTGATACAAGTGTACTTGTGAGGCTAAGACCTGCATGGGAGGACCTCCGGAGCTACCTAACTGCAAGGGGGCGCAAGCGTTTTGAGGTTTATGTTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agcagatagatttgtcagaatcattagtctaacaaaaatttgcgtgtttgggaagATTCGTGATACGAGTGTTCTTGTGAGGTTGAGACCTGCATGGGAAGATCTTCGGAGCTACTTGACTGCAAGAGGGCGCAAGCGTTTTGAGGTTTATGTCT
gtctaac putative branch site (score: 2)
tctaacaaaaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ataaatagataagctgtgttttatctattttatctaaaatatacaagcagatagatttgtcagaatcattagtctaacaaaaatttgcgtgtttgggaagATTCGTGATACGAGTGTTCTTGTGAGGTTGAGACCTGCATGGGAAGATCTTCGGAGCTACTTGACTGCAAGAGGGCGCAAGCGTTTTGAGGTTTATGTCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - gctgtgt
- - - - - - - - - - - - - - - - - - - - -tacaagc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aacaaaa