Sequence
atgc intronic sequence ATGC exonic sequence...ttcagaaattgtgttgctcttgtttcggatccatggttatgagtcttttaatgggtgtgctccatccatggttacacacttaaacagtttcttttgtcagGTTATCAGCCGAGTTGGCGATCTTGTTGGTATAAAATACTTCCCTGCGCAGCCCAAGGAGCAGCAACAAGAGGAAAAAACATCAAAACTGGACTGAAAGT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv14s0068g01300.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: LOC_Os11g31640.1 (Oryza sativa), 3'ss of exon 11
ttcagaaattgtgttgctcttgtttcggatccatggttatgagtcttttaatgggtgtgctccatccatggttacacacttaaacagtttcttttgtcagGTTATCAGCCGAGTTGGCGATCTTGTTGGTATAAAATACTTCCCTGCGCAGCCCAAGGAGCAGCAACAAGAGGAAAAAACATCAAAACTGGACTGAAAGT---
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gtgagtgctttcgtttgttaattttcggct----gttcacatatgtttaaacggat---tccaattcacatt---gttctcatgtttgtaatccactcagGTTATCAGCAGAGTTGGTGATCTTGTGGGCATCAAGTACTTCCCTGCGGAGCCGCCAAAG--ATTGCTGAAGCTGATCACGATAAG-CTGGAGTAAATGATGA
upper sequence: Vv14s0068g01300.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GRMZM2G067257_T01 (Zea mays), 3'ss of exon 12
ttcagaaattgtgttgctcttgtttcggatccatggttatgagtcttttaatgggtgtgctccatccatg-gttacacacttaaacagtttcttttgtcagGTTATCAGCCGAGTTGGCGATCTTGTTGGTATAAAATACTTCCCTGCGCAGCCCAAGGAGCAGCAACAAGAGGAAAAAACATCAAAACTGGACTGAAAGT
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------gtgagtgttataaatacttcatttttatt-ctaggagtcata-aataaa---gctgagttgatgtgtttcttgtctgtgcaacccactct--cagGTTATCAGCAGAGTTGGCGACCTTGTGGGCATCAAATACTTCCCTGCAGAACCACCAAAG--ATTGCTGGAGCTGATCATGATAAG-CTGGAGTAG----
upper sequence: Vv14s0068g01300.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GRMZM2G152888_T01 (Zea mays), 3'ss of exon 11
ttcagaaattgtgttgctcttgtttcggatccatggttatgagtcttttaatgggtgtgctccatccatg-gttacacacttaaacagtttcttttgtcagGTTATCAGCCGAGTTGGCGATCTTGTTGGTATAAAATACTTCCCTGCGCAGCCCAAGGAGCAGCAACAAGAGGAAAAAACATCAAAACTGGACTGAAAGT---
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------gtgagtgttataaatacttcatttttatt-ctaggagtcata-aataga---gccgagctgatgtgtttcttgtctgtgcaacccactct--cagGTTATCAGCAGAGTTGGCGACCTTGTGGGCATCAAATACTTCCCTGCAGAACCACCAAAG--ATTGCTGGAGCTGATCATGATAAG-CTGGAGTAGGAATCAA
upper sequence: Vv14s0068g01300.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GRMZM2G357734_T03 (Zea mays), 3'ss of exon 16
ttcagaaattgtgttgctcttgtttcggatccatggttatgagtcttttaatgggtgtgctccatccatg-gttacacacttaaacagtttcttttgtcagGTTATCAGCCGAGTTGGCGATCTTGTTGGTATAAAATACTTCCCTGCGCAGCCCAAGGAGCAGCAACAAGAGGAAAAAACATCAAAACTGGACTGAAAGT
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------gtgagtgttataaatacttcatttttatt-ctaggagtcata-aataaa---gctgagctgatgtgtttcttgtctgtgcaacccactct--cagGTTATCAGCAGAGTTGGCGACCTTGTGGGCATCAAATACTTCCCTGCAGAACCACCAAAG--ATTGCTGGAGCTGATCATGATAAG-CTGGAGTAG----
upper sequence: Vv14s0068g01300.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GRMZM2G142030_T01 (Zea mays), 3'ss of exon 11
ttcagaaat-tgtgttgctcttgtttcggatccatggttatgagtcttttaatgggtgtgctccatccatg-gttacacacttaaacagtttcttttgtcagGTTATCAGCCGAGTTGGCGATCTTGTTGGTATAAAATACTTCCCTGCGCAGCC-CAAGGAGCAGCAACAAGAGGAAAAAACATCAAAACTGGACTGAAAGT---
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gtgagtgctgtatcttgtttttttttggcataaatacttcatttcattctgggtgacataacgaactgatgtgtttcctgtctgcgcaacccacttc--cagGTTATCAGCAGAGTTGGTGATCTTGTGGGCATCAAATACTTCCCTGCAGAACCACCAAAGATTGCTGAAGCTGGTCATGATA----AGCTGGAGTAGGAGCGAA
upper sequence: Vv14s0068g01300.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GRMZM2G137556_T01 (Zea mays), 3'ss of exon 6
ttcagaaattgtgttgctcttgtttcggatccatggttatgagtct---tttaatgggtgt-gctccatccatg-gttacacacttaaacagtttcttttgtcagGTTATCAGCCGAGTTGGCGATCTTGTTGGTATAAAATACTTCCCTGCGCAGCCCAAGGAGCAGCAACAAGAGGAAAAAACATCAAAACTGGACTGAAAGT---
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---aaagcccttgatgtcagtgttataaatacttcatttttattctaggagtcataaataaagctgagctgatgtgtttcttgtctgtgcaacccactct--cagGTTATCAGCAGAGTTGGCGACCTTGTGGGCATCAAATACTTCCCTGTAGAACCACCAAAG--ATTGCTGGAGCTGATCATGATAAG-CTGGAGTAGGAATCAA
upper sequence: Vv14s0068g01300.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GRMZM2G157249_T01 (Zea mays), 3'ss of exon 4
ttcagaaattgtgttgctcttgtttcggatccatggttatgagtcttttaatgggtgtgctccatccatg-gttacacacttaaacagtttcttttgtcagGTTATCAGCCGAGTTGGCGATCTTGTTGGTATAAAATACTTCCCTGCGCAGCCCAAGGAGCAGCAACAAGAGGAAAAAACATCAAAACTGGACTGAAAGT---
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------gtgagtgttataaatacttcatttttatt-ctaggagtcata-aataaa---gccgagctgatgtgtttcttgtctgtgcaacccactct--cagGTTATCAGCAGAGTTGGTGACCTTGTGGGCATCAAATACTTCCCTGCAGAAACACCAAAG--ATTGCTGGAGCTGATCATGATAAG-CTGGAGTAGGAATCAA
upper sequence: Vv14s0068g01300.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA16G26210.1 (Glycine max), 3'ss of exon 11
--ttcagaaattgtgttgctcttgtttcggatccatggttatgagtcttttaatgggtgtgctccatccatggttacacact-taaacagtttcttttgtcagGTTATCAGCCGAGTTGGCGATCTTGTTGGTATAAAATACTTCCCTGCGCAGCCCAAGGAGCAGCAACAAGAGGAA---AAAACATCAAAACTGGACTGAAAGT
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attttgtttgttttgatatacttcttacagggattttgtt-taaatttgctatttc-catgatatgtt-gtgttaatttgctatgatcttctttctttcttagGTTATTAGCAGAGTGGGTGATCTTGTTGGCATAAAATACTTCCCTGCTGAACCAACAAAGCAGCAACAAGAAGGGGGTAAAACTGTGAAGTTTGATTGAG---
upper sequence: Vv14s0068g01300.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA02G07250.1 (Glycine max), 3'ss of exon 11
ttcagaaattgtgttgctcttgtttcggatccatggttatgagtcttttaatgggtgtgctccatccatggttacacact-taaacagtttcttttgtcagGTTATCAGCCGAGTTGGCGATCTTGTTGGTATAAAATACTTCCCTGCGCAGCCCAAGGAGCAGCAACAAGAGGAAAAAACATCAAAACTGGACTGAAAGT
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-ttgtttgttttgatatgcttcttacagggttttgtttaaatttgctacttccatgataggttttgtgtggtaatttgctatgattgttcttctttgttagGTTATTAGCAGAGTGGGTGATCTTGTTGGCATAAAATATTTCCCTGCTGAACCAACAAAGCAGCAACAAGGGGGTAAATCTGTGAAGTTTGATTGAGAGAMapped 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|352778117|gb|FQ467170.1|FQ467170EST: TCTGCATATCTGCATCTCATACCAAAGAAGACCTGATTAAAGGCTTGGAG GTTATCAGCCGAGTTGGCGATCTTGTTGGTATAAAATACTTCCCTGCGCAG
genomic: TCTGCATATCTGCATCTCATACCAAAGAAGACCTGATTAAAGGCTTGGAGgtaatttgat ... cttttgtcagGTTATCAGCCGAGTTGGCGATCTTGTTGGTATAAAATACTTCCCTGCGCAG
EST:
gi|352789616|gb|FQ476214.1|FQ476214EST: TCTGCATATTTGCATCTCATACCAAAGAAGACCTGATTAAAGGCTTGGAG GTTATCAGCCGAGTTGGCGATCTTGTTGGTATAAAATACTTCCCTGCGCAG
genomic: TCTGCATATCTGCATCTCATACCAAAGAAGACCTGATTAAAGGCTTGGAGgtaatttgat ... cttttgtcagGTTATCAGCCGAGTTGGCGATCTTGTTGGTATAAAATACTTCCCTGCGCAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttaatgggtgtgctccatccatggttacacacttaaacagtttcttttgtcagGTTATCAGCCGAGTTGGCGATCTTGTTGGTATAAAATACTTCCCTGCGCAGCCCAAGGAGCAGCAACAAGAGGAAAAAACATCAAAACTGGACTGAAAGT
ttttaat putative branch site (score: 3)
tttcttttgtc putative PPT
tttctttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttcagaaattgtgttgctcttgtttcggatccatggttatgagtcttttaatgggtgtgctccatccatggttacacacttaaacagtttcttttgtcagGTTATCAGCCGAGTTGGCGATCTTGTTGGTATAAAATACTTCCCTGCGCAGCCCAAGGAGCAGCAACAAGAGGAAAAAACATCAAAACTGGACTGAAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- -agaaatt
- - - - - - - -gctcttg
- - - - - - - - - - - - - - - ccatggt
- - - - - - - - - - - - - - - - - - - - - - - - - - gggtgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tacacac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaacagt