Sequence
atgc intronic sequence ATGC exonic sequencegtaaatatatgattccaattcaaacaaatttacctatttcgtgataagctcatatgcaatttattctgcaaccagcctctgtttattgtcacttgttttatcttcataggtgtgcagccttatattatcctgtcttttttcttacatacaatctactgtagGTATATGCGGCCAGAGACAGCACAGGGCATTTTTGTAAACTTCAAGGATCTGTATTACTATAATGGGAACAAGCTCCCTTTTGCTGCAGCTCAAATTGGT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv17s0000g00160.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os04g32650.1 (Oryza sativa), 3'ss of exon 2
gtaaatatatgattccaattcaaacaaatttacctatttcgtgataagctcatatgcaatttattctgcaaccagcctctgtttattgtcacttgttttatcttcataggtgtgcagccttatattatcctgtcttttttcttacatacaatcta---ctgtagGTATATGCGGCCAGAGACAGCACAGGGCATTTTTGTAAACTTCAAGGATCTGTATTACTATAATGGGAACAAGCTCCCTTTTGCTGCAGCTCAAATTGGT
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-------------------------------------------------------------------------------------gtgaggtcaagaacagctcaatatttttgta-cttcat-ttattctg-ctttaaacttatgtgcttcctcggtttttagGTATATGAGGCCAGAGACAGCACAAGGTATCTTTGTAAACTTCAAAGACTTGTATTACTACAACGGCAACAAGCTACCCTTTGCTGCAGCACAGATTGGT
upper sequence: Vv17s0000g00160.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os08g42560.1 (Oryza sativa), 3'ss of exon 2
gtaaatatatgattccaattcaaacaaatttacctatttcgtgataagctcatatgcaatttattctgcaaccagcctctgtttattgtcacttgttttatcttcataggtgtgcagccttatattatcctgtcttttttcttacatacaatctactgtagGTATATGCGGCCAGAGACAGCACAGGGCATTTTTGTAAACTTCAAGGATCTGTATTACTATAATGGGAACAAGCTCCCTTTTGCTGCAGCTCAAATTGGT
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----------------------------------------gtaagaatatca-atgttcactttttttaacccaaga---gattaatgttcactgtttaattct-gttgttatgctgattggc-tgaatgtgttcaattttgtgtgaacaaac------agGTATATGAGACCAGAAACAGCACAGGGTATTTTTGTCAACTTCAAGGACTTGTACTATTACAACGGGCAAAAGCTCCCTTTCGCAGCAGCTCAAATCGGG
upper sequence: Vv17s0000g00160.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM5G821551_T03 (Zea mays), 3'ss of exon 2
gtaaatatatgattccaattcaaacaaatttacctatttcgtgataagctcatatgcaatttattctgcaaccagcctctgtttattgtcacttgttttatcttcataggtgtgcagccttatattatcctgtcttttttcttacatacaatctactgtagGTATATGCGGCCAGAGACAGCACAGGGCATTTTTGTAAACTTCAAGGATCTGTATTACTATAATGGGAACAAGCTCCCTTTTGCTGCAGCTCAAATTGGT
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----------------------------------------------------------------------gtgagaatatctccattctctctgtggttatgttccttt-tgtgttgattggctaaaaaggttcaattttgtgtggcggaa------atagGTATATGCGACCAGAGACCGCACAGGGTATTTTTGTAAACTTCAAGGATCTGTACTATTACAATGGCCAAAAGCTCCCTTTTGCAGCTGCTCAAATTGGG
upper sequence: Vv17s0000g00160.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G041797_T01 (Zea mays), 3'ss of exon 2
gtaaatatatgattccaattcaaacaaatttacctatttcgtgataagctcatatgcaatttattctgcaaccagcctctgtttattgtcacttgttttatcttcataggtgtgcagccttatattatcctgtcttttttcttacatacaatctactgtagGTATATGCGGCCAGAGACAGCACAGGGCATTTTTGTAAACTTCAAGGATCTGTATTACTATAATGGGAACAAGCTCCCTTTTGCTGCAGCTCAAATTGGT
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-------------------------------------------gtaagaatatgtccattctgt-ctgcaattatgttccttttgtggtgatttg------ctaaaaaaaggtccaattttgtgtgg-------------------------cggaaatagGTATATGCGACCAGAGACAGCACAGGGTATTTTTGTAAATTTCAAGGATCTATACTATTACAATGGCCAAAAGCTCCCCTTTGCAGCTGCTCAAATTGGG
upper sequence: Vv17s0000g00160.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G171688_T01 (Zea mays), 3'ss of exon 2
gtaaatatatgattccaattcaaacaaatttacctatttcgtgataagctcatatgcaatttattctgcaaccagcctctgtttattgtcacttgttttatcttcataggtgtgcagccttatattatcctgtcttttttcttacatacaatctactgtagGTATATGCGGCCAGAGACAGCACAGGGCATTTTTGTAAACTTCAAGGATCTGTATTACTATAATGGGAACAAGCTCCCTTTTGCTGCAGCTCAAATTGGT
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---------------------------------------------------gtaagacaataacggctgaataaatttcagtatatttccact------atgttcat-------ccggcttaagtgtatctgcttccttggtt------------ttgcagGTATATGAGGCCAGAGACAGCTCAGGGTATATTTGTGAACTTCAAAGACTTGTATTACTACAATGGCAATAAGCTGCCATTCGCTGCAGCCCAAATTGGT
upper sequence: Vv17s0000g00160.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: PP1S310_3V6.1 (Physcomitrella patens), 3'ss of exon 1
gtaaatatatgattccaattcaaacaaatttacctatttcgtgataagctcatatgcaatttattctgcaaccagcctctgtttattgtcacttgttttatcttcataggtgtgcagccttatat-tatcctgtcttttttcttacatacaatctactgtagGTATATGCGGCCAGAGACAGCACAGGGCATTTTTGTAAACTTCAAGGATCTGTATTACTATAATGGGAACAAGCTCCCTTTTGCTGCAGCTCAAATTGGT
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---------------------------------------------------gtaagagtcctaaccttggttt--cttccctttggagtccattacgtgaagcttgaatgctcgcaaactgaaacctgtggggtcttctgtccaaca--------------gTTATATGAGGCCGGAGACAGCACAAGGCATTTTTGTGAACTTCAGGGATTTGTACTACGAAAGTGGTAATAAGCTGCCTTTCGCTGCAGCCCAGATTGGTMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|352781854|gb|FQ469152.1|FQ469152EST: TTCAATTTGATGTTCCAGACCTCAATCGGCCCATCTGGCTTGAGCCCAGG GTATATGCGGGCAGAGACAGCACAGGGCATTTTTGTAAAC
genomic: TTCAATTTGATGTTCCAGACCTCAATCGGCCCATCTGGCTTGAGCCCAGGgtaaatatat ... tctactgtagGTATATGCGGCCAGAGACAGCACAGGGCATTTTTGTAAAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taggtgtgcagccttatattatcctgtcttttttcttacatacaatctactgtagGTATATGCGGCCAGAGACAGCACAGGGCATTTTTGTAAACTTCAAGGATCTGTATTACTATAATGGGAACAAGCTCCCTTTTGCTGCAGCTCAAATTGGT
ttcttac putative branch site (score: 2)
ttttttcttacata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaatatatgattccaattcaaacaaatttacctatttcgtgataagctcatatgcaatttattctgcaaccagcctctgtttattgtcacttgttttatcttcataggtgtgcagccttatattatcctgtcttttttcttacatacaatctactgtagGTATATGCGGCCAGAGACAGCACAGGGCATTTTTGTAAACTTCAAGGATCTGTATTACTATAATGGGAACAAGCTCCCTTTTGCTGCAGCTCAAATTGGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA