Sequence
atgc intronic sequence ATGC exonic sequence...ttagtaatatggtggtgatctgaaatccaaccacagaaataaaagcttagcaaaaaaaaatcagtttccagtttgactgagagatctccactttttgcagCCTCAAGCAAGGGAAAAAGCTGAAAAGGAGGGATTTGAAGTAAGTGTTGCCAAGACTGGTTTTAAGGCTAACACAAAGGTCCTAGCCGAAAATGAAGGGG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv14s0060g01330.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: LOC_Os05g06460.1 (Oryza sativa), 3'ss of exon 11
ttagtaatatggtggtgatctgaaatc-caaccacagaaataaaagcttagcaaaaaaaaatcagtttccagtttgactgagag--atctccactttttgcagCCTCAAGCAAGGGAAAAAGCTGAAAAGGAGGGATTTGAAGTAAGTGTTGCCAAGACTGGTTTTAAGGCTAACACAAAGGTCCTAGCCGAAAATGAAGGGG
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-ttttactgtatt--tggtatgtatccattgcttcttgaaggggatctaaaccatgcaatctttatgatttccttgaccaagtgttatcaataaatattgcagCCACAAGCCAGAGAAAAAGCTGATAAAGAAGGATTTGAGATAAGTGTTGTTAAGACCAGCTTTAAGGCTAATACAAAAGCATTGGCAGAAAATGAAGGAG
upper sequence: Vv14s0060g01330.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GRMZM2G145595_T01 (Zea mays), 3'ss of exon 11
-----------------------------------------------------------------------------------------ttagtaatatggtggtgatctgaaatccaaccacagaaataaaagcttagcaaaaaaaaatcagtttccagtttgactgagagatctccactttttgcagCCTCAAGCAAGGGAAAAAGCTGAAAAGGAGGGATTTGAAGTAAGTGTTGCCAAGACTGGTTTTAAGGCTAACACAAAGGTCCTAGCCGAAAATGAAGGGG
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gtaagtgagataccattctccaatattacattctctgttcaacatagttgaaatctgcttggtaaagttaatttgactagtacactttcttaagtataaaatcacaacttgtt-tccaactcttgctttgcttggctagcaaaccaa--tc--tttacgactctaatcattg--ttcctgcttttgcagCCACAGGCTAGGGAGAAGGCTGACAAGGAAGGATTTGAAATAAGTGTTGTAAAGACCAGTTTTAAGGCTAACACAAAGGCCCTGGCAGAGAATGAAGGAG
upper sequence: Vv14s0060g01330.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: PP1S352_68V6.1 (Physcomitrella patens), 3'ss of exon 11
-------------------------------------------ttagtaatatggtggtgatctgaaatccaaccacagaaataaaagcttagcaaaaaaaaatcagtttccagtttgactgagagatctc----cactttttg-cagCCTCAAGCAAGGGAAAAAGCTGAAAAGGAGGGATTTGAAGTAAGTGTTGCCAAGACTGGTTTTAAGGCTAACACAAAGGTCCTAGCCGAAAATGAAGGGG
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gtgatggtttgggtcactgcttacaattctatatttgtgaggttttaccgcttagaatatttcaagagttttttcacgtggagatcagctgtaatagatcgcatcgtacagaagtgaagtttcttaatttctgagcatttcatgacagCCTCAAGCACGAGCACTAGCTGAAAAGGAGGGATTCAAAGTAAGCGTTGCCAAGACCAGCTTCAAAGCCAATACCAAGGCACTAGCTGAAAACGAGGGTGMapped 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|110371471|gb|EC935522.1|EC935522EST: CAGCAGCGTGTTTCACCCATCCTGAGATCAGTATGGTGGGGCTGACAGAG CCTCAAGCAAGGGAAAAAGCTGAAAAGGAGGGATTTGAAGTAAGTGTTGCC
genomic: CAGCAGCGTGTTTCACCCATCCTGAGATCAGTATGGTGGGGCTGACAGAGgtaattctgt ... ctttttgcagCCTCAAGCAAGGGAAAAAGCTGAAAAGGAGGGATTTGAAGTAAGTGTTGCC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttagcaaaaaaaaatcagtttccagtttgactgagagatctccactttttgcagCCTCAAGCAAGGGAAAAAGCTGAAAAGGAGGGATTTGAAGTAAGTGTTGCCAAGACTGGTTTTAAGGCTAACACAAAGGTCCTAGCCGAAAATGAAGGGG
gtttgac putative branch site (score: 4)
tctccactttttgc putative PPT
aaaaaaaaatcagttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttagtaatatggtggtgatctgaaatccaaccacagaaataaaagcttagcaaaaaaaaatcagtttccagtttgactgagagatctccactttttgcagCCTCAAGCAAGGGAAAAAGCTGAAAAGGAGGGATTTGAAGTAAGTGTTGCCAAGACTGGTTTTAAGGCTAACACAAAGGTCCTAGCCGAAAATGAAGGGG
- - - - - ggtggtg
- - - - - - - - - - - - - ccaacca
- - - - - - - - - - - - - - - - - - aaataaa
- - - - - - - - - - - - - - - - - - - - - - - - - -aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgactga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atctcca