Sequence
atgc intronic sequence ATGC exonic sequencegtaaatcatatatctatttgcaagtgatgcagcttccctccactttttccccagtcattcatcacaacattgtgtccttggtctgatctctgatcattctgcatgttctatagAGGTGCTTGTGCATCAGTCTGGGAGAACTTCAAGAACAACCCGCTCTTCGACATCTCGACTGATCACCCACCAACTTACTACGAAGACATGCAGCGTTCA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G141094_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g70200.1 (Oryza sativa), 3'ss of exon 3
gtaaatcatatatctatttgcaagtgatgcagcttccctccactttttccccagtcattcatcacaacattgtgtccttg-gtctgatctctgatcattctgcatgttctat-agAGGTGCTTGTGCATCAGTCTGGGAGAACTTCAAGAACAACCCGCTCTTCGACATCTCGACTGATCACCCACCAACTTACTACGAAGACATGCAGCGTTCA
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--------------------------gtaaattttccgcttatctccaatacatcctatcatctgctcattggctcgtagcatgtggagtctgatgtttctgtatgtcctatcagAGGTGCCCGCGCGTCGGTTTGGGAGAATTTCAAGAACAACCCGCTGTTTGACATCTCAACCGATCACCCACCCACGTACTACGAAGATATGCAGAGATCT
upper sequence: GRMZM2G141094_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA05G33420.1 (Glycine max), 3'ss of exon 3
gtaaatcatatatctatttgcaagtgatgcagcttccct--ccactttttccccagtcattcatcacaacattgtgtccttggtctgatctctgatcattctgcatgttctatagAGGTGCTTGTGCATCAGTCTGGGAGAACTTCAAGAACAACCCGCTCTTCGACATCTCGACTGATCACCCACCAACTTACTACGAAGACATGCAGCGTTCA
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-------atgaagtttggtgcatgcaatgatgctttcataacaaaacacacttggatcaacaa--ataatcctggttgatgaaactgaccgt-----gttttgca-atcttgcagAGGCGCAAGAGCAGCAGTGTGGGAGAACTTTAAGGACAATCTGCTGTTTGACATCTCCACTGAGCATCCAACCACTTACTACGAGGACATGCAAAGAGCC
upper sequence: GRMZM2G141094_T02 (Zea mays), 3'ss of exon 2
lower sequence: AT1G27440.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaaatcatatatctatttgcaagtgatgcagcttccctccactttttccccagtcattcatcacaacattgtgtccttggtctgatctctgatcattctgcatgttctatagAGGTGCTTGTGCATCAGTCTGGGAGAACTTCAAGAACAACCCGCTCTTCGACATCTCGACTGATCACCCACCAACTTACTACGAAGACATGCAGCGTTCA
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-acaattaagcat-tcctcattaggaagttaggttatatataa---------ggttagctaagatcaaattgt-tttagaatctgctgactggaacttct-ctctttgtatagAGGTGCAAGAGCAGCGGTGTGGGAGAACTTCAAGAACAACCCTTTGTTTGACATCTCAACAGATCACCCGACAACATACTACGAAGACATGCAGAGAGCC
upper sequence: GRMZM2G141094_T02 (Zea mays), 3'ss of exon 2
lower sequence: Vv01s0150g00180.t01 (Vitis vinifera), 3'ss of exon 3
gtaaatcatatatctatttgcaagtgatgcagcttccctccactttttccccagtcattcatcacaacattgtgtccttggtctgatctctgatcattctgcatgttctatagAGGTGCTTGTGCATCAGTCTGGGAGAACTTCAAGAACAACCCGCTCTTCGACATCTCGACTGATCACCCACCAACTTACTACGAAGACATGCAGCGTTCA
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----aggaagcaacatcttgtatgatacatggctttgtc---ttttatattaggtccttt------gggttgaatgaatcaactcctatctaactcttttaattgattgacagAGGTGCAAGGGCAGCAGTTTGGGAGAACTTTAAGGACAACCCGCTCTTTGACATCTCCACTGAGCACCCAACGACATATTATGAAGACATGCAACGTGCT
upper sequence: GRMZM2G141094_T02 (Zea mays), 3'ss of exon 2
lower sequence: PP1S7_455V6.1 (Physcomitrella patens), 3'ss of exon 4
gtaaatcatatatctatttgcaagtgatgcagcttccctccactttttccccagtcattcatcacaacattgtgtccttggtctgatctctga-----tcattctgc-atgttctatagAGGTGCTTGTGCATCAGTCTGGGAGAACTTCAAGAACAACCCGCTCTTCGACATCTCGACTGATCACCCACCAACTTACTACGAAGACATGCAGCGTTCA
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-------------------gcatgcaagctagtttttattcatcttttgtgtatttattcttttgcttcctcttggtttgttagacatactgagttcttcattggatgattctttgcagAGGCGCAAGAGCAGCTATCTGGGAAAATTTCAAAGATAACCCATTGTTCGACATCTCGACAGAGCATCCAGCAACTTACTATGAAGACATGCAACGCGCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcatcacaacattgtgtccttggtctgatctctgatcattctgcatgttctatagAGGTGCTTGTGCATCAGTCTGGGAGAACTTCAAGAACAACCCGCTCTTCGACATCTCGACTGATCACCCACCAACTTACTACGAAGACATGCAGCGTTCA
ctctgat putative branch site (score: 4)
ttctata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaatcatatatctatttgcaagtgatgcagcttccctccactttttccccagtcattcatcacaacattgtgtccttggtctgatctctgatcattctgcatgttctatagAGGTGCTTGTGCATCAGTCTGGGAGAACTTCAAGAACAACCCGCTCTTCGACATCTCGACTGATCACCCACCAACTTACTACGAAGACATGCAGCGTTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA