Sequence
atgc intronic sequence ATGC exonic sequencegttttctttatctttttttttataaatttatttttcttatatttccccgtgaattgctctttttgatcatgatcaaagtcaacattattatcaaaaggttggtttgttaactttttcttaacaacagGTGGGCTCAGATAGCCAAGCACCTACCTGGAAGAACAGATAATGAGGTGAAGAACTTTTGGAATTCAAGCATAAAGAAGAAGCTGCTTTCTCATGATGTT
Basic information
species | Glycine max |
transcript | GLYMA13G42430.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G42430.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g51260.1 (Oryza sativa), 3'ss of exon 2
gttttctttatctttttttttataaatttatttttcttatatttccccgtg-aattgctctttttgatcatgatcaaagtcaacattattatcaaaaggttggtttgttaactttttcttaaca-acagGTGGGCTCAGATAGCCAAGCACCTACCTGGAAGAACAGATAATGAGGTGAAGAACTTTTGGAATTCAAGCATAAAGAAGAAGCTGCTTTCTCATGATGTT
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--------------------------ttgatctgagacaaaggacggggcgcaaatgtggcaatcgatcgagatttgagctggc--taacat-atgctgtgtcactgtgattcactgcattgcatgcagGTGGGCTCAGATTGCCAAGCACCTACCTGGTAGAACAGACAATGAGGTCAAGAACTTCTGGAACTCCACCATCAAGAAGAAGCTCATCTCCCAGGCCGTG
upper sequence: GLYMA13G42430.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G088783_T01 (Zea mays), 3'ss of exon 2
gttttctttatctttttttttataaatttatttttcttatatttccccgtgaattgctctttttgatcatgatcaaagtcaacattattatcaaaaggt-tggtttgttaac------tttttcttaaca-acagGTGGGCTCAGATAGCCAAGCACCTACCTGGAAGAACAGATAATGAGGTGAAGAACTTTTGGAATTCAAGCATAAAGAAGAAGCTGCTTTCTCATGATGTT
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-----------------------------------catatgtcgccttaataacttgcttgggagtttgggacaaaggaaagagacgcgaatggaaaatgcagctagctaaaaatgcgtgccactgcacacacagGTGGGCCCAGATCGCCAAGCATCTGCCTGGTAGAACGGACAACGAGGTGAAGAACTTCTGGAACTCCACCATCAAGAAGAAGCTCATCTCCCAGGCCGTG
upper sequence: GLYMA13G42430.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G13890.2 (Arabidopsis thaliana), 3'ss of exon 2
gttttctttatctttttttttataaatttatttttcttatatttccccgtgaattgctctttttgatcatgatcaaagtcaacattattatcaaaaggttggtttgttaactttttcttaacaacagGTGGGCTCAGATAGCCAAGCACCTACCTGGAAGAACAGATAATGAGGTGAAGAACTTTTGGAATTCAAGCATAAAGAAGAAGCTGCTTTCTCATGATGTT
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-----------------gtttgtcagttcattaacatt---tatacatgtgaaatacaaaact--aacatttct----tcaagactttgacttact--ttttttaatcatgttatggtttttgacagATGGGCTCAAATTGCTAAACATCTACCTGGAAGAACAGATAACGAGGTCAAGAATTTCTGGAACTCGAGCATTAAAAAGAAGCTCATGTCTCACCATCAT
upper sequence: GLYMA13G42430.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv09s0002g01670.t01 (Vitis vinifera), 3'ss of exon 2
gttttctttatctttttttttataaatttatttttcttatatttccccgtgaattgctctttttgatcatgatcaaagtcaacattattatcaaaaggttggtttgttaactttttcttaacaacagGTGGGCTCAGATAGCCAAGCACCTACCTGGAAGAACAGATAATGAGGTGAAGAACTTTTGGAATTCAAGCATAAAGAAGAAGCTGCTTTCTCATGATGTT
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--------------gtacttgataa--ctattttgccttcatatc----tgatttattctttctttccatg--caaagac----tgattttca---------tcttcttatttttcttt--ctgcagATGGGCTCAGATAGCTAAGCACTTACCAGGGAGAACAGATAATGAAGTGAAGAACTTTTGGAATTCAAGCATAAAGAAGAAGCTAGTCTCTCATGGTGTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcaaagtcaacattattatcaaaaggttggtttgttaactttttcttaacaacagGTGGGCTCAGATAGCCAAGCACCTACCTGGAAGAACAGATAATGAGGTGAAGAACTTTTGGAATTCAAGCATAAAGAAGAAGCTGCTTTCTCATGATGTT
tcttaac putative branch site (score: 2)
ctttttctt CT-rich tract
aacattattatcaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttttctttatctttttttttataaatttatttttcttatatttccccgtgaattgctctttttgatcatgatcaaagtcaacattattatcaaaaggttggtttgttaactttttcttaacaacagGTGGGCTCAGATAGCCAAGCACCTACCTGGAAGAACAGATAATGAGGTGAAGAACTTTTGGAATTCAAGCATAAAGAAGAAGCTGCTTTCTCATGATGTT
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT