Sequence
atgc intronic sequence ATGC exonic sequence...aacatgaatggatggtacatgttttctgtagtttcttataattaaaacatgtagacttgtcagaatcattggtccaacaataacttgtgtctttggaaagATTCGTGATACTAGTGTTCTTGTGAGGTTGAGACCTGCATGGGAAGATCTCCGGAGCTACCTGACTGCAAGAGGGCGCAAGCGTTTTGAGGTTTTTGTTT
Basic information
species | Glycine max |
transcript | GLYMA13G31510.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G31510.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os04g44710.2 (Oryza sativa), 3'ss of exon 3
aacatgaatggatggtacatgttttctgtagtttcttataattaaa--acatgtagacttgtcagaatcattggtccaacaataa-cttgtgtctttggaaagATTCGTGATACTAGTGTTCTTGTGAGGTTGAGACCTGCATGGGAAGATCTCCGGAGCTACCTGACTGCAAGAGGGCGCAAGCGTTTTGAGGTTTTTGTTT
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--gagcgctaagcacttcccgtctattcagctttgatacaaccatgttccatgtttccatgctgttat-actgcctagttgattttccctttttcttaattagATAAGAGATACCAGTGTTCTGGTACGGTTGAGGCCTGCATGGGAGGATCTTCGGAGCTACTTAATTGCAAGAGGTCGCAAACGTTTTGAGGTATATGTGT
upper sequence: GLYMA13G31510.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os02g42600.1 (Oryza sativa), 3'ss of exon 2
-aacatgaatggatggtacatgttttctgtagtttcttataattaaaacatgtagacttgt-cagaatcattggtccaacaataacttgtgtctt---tggaaagATTCGTGATACTAGTGTTCTTGTGAGGTTGAGACCTGCATGGGAAGATCTCCGGAGCTACCTGACTGCAAGAGGGCGCAAGCGTTTTGAGGTTTTTGTTT
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cagcgtgcct---tttcacat-tgctttgatgtggcctg-actttggttgcataagtttgtacaaaacttccaggctaaggctttttttttttttttttgtgtagATAAGGGATACCAGTGTTCTTGTACGTTTAAGGCCAGCATGGGAGGATCTCCGGAGCTACTTGATTGCTAGAGGTCGCAAACGTTTTGAGGTCTATGTGT
upper sequence: GLYMA13G31510.1 (Glycine max), 3'ss of exon 2
lower sequence: AT4G21670.1 (Arabidopsis thaliana), 3'ss of exon 2
aacatgaatggatggtacatgttttctgtagtttcttataattaaaacatgtagacttgtcagaatcattg-gtccaacaataa---cttgtgtctttggaaagATTCGTGATACTAGTGTTCTTGTGAGGTTGAGACCTGCATGGGAAGATCTCCGGAGCTACCTGACTGCAAGAGGGCGCAAGCGTTTTGAGGTTTTTGTTT
||| | | | || | | || || | | | || |||| || || |||| ||| | | | | | | | | | | ||||||||||||| |||||||||||||| |||| || ||||||| || || || ||||| |||| |||| |||||| ||||||||||| || | |||||
----cttgtggtataaccttttatttttcatttgctcctttctggagcacctagatttttctgaattcttgtggctgaatctgcattcctatatttacacacagATTCGTGATACAAGTGTTCTTGTGAGAATGAGGCCCTCATGGGAGGAACTTCGAAGCTATTTGACAGCAAAAGGGCGTAAGCGTTTTGAAGTATATGTTT
upper sequence: GLYMA13G31510.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv00s0370g00040.t01 (Vitis vinifera), 3'ss of exon 2
--aacatga-atggatggtacatgttttctgtagtttcttataattaaaacatgtagacttgtcagaatcattggtccaacaataacttgtgtctttggaaagATTCGTGATACTAGTGTTCTTGTGAGGTTGAGACCTGCATGGGAAGATCTCCGGAGCTACCTGACTGCAAGAGGGCGCAAGCGTTTTGAGGTTTTTGTTT
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ataccactatacttcttgtttatgtcatccaataagcctgtaaactcattccaagaaactggtttgt-ttagtgacacaaaatttttttatatctcc--acagATTCGTGATACAAGTGTACTTGTGAGGCTAAGACCTGCATGGGAGGACCTCCGGAGCTACCTAACTGCAAGGGGGCGCAAGCGTTTTGAGGTTTATGTTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aacatgtagacttgtcagaatcattggtccaacaataacttgtgtctttggaaagATTCGTGATACTAGTGTTCTTGTGAGGTTGAGACCTGCATGGGAAGATCTCCGGAGCTACCTGACTGCAAGAGGGCGCAAGCGTTTTGAGGTTTTTGTTT
caataac putative branch site (score: 2)
tgtcttt putative PPT
aacaataa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aacatgaatggatggtacatgttttctgtagtttcttataattaaaacatgtagacttgtcagaatcattggtccaacaataacttgtgtctttggaaagATTCGTGATACTAGTGTTCTTGTGAGGTTGAGACCTGCATGGGAAGATCTCCGGAGCTACCTGACTGCAAGAGGGCGCAAGCGTTTTGAGGTTTTTGTTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
-acatgaa
- - - - tggatgg
- - - - - - - -tacatgt
- - - - - - - - - - - -ttctgta
- - - - - - - - - - - - - - - - - - - - - - - acatgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - -cttgtca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccaacaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acttgtg