Sequence
atgc intronic sequence ATGC exonic sequence...cttgtgtctgttcagcaattctagtcccagacacgtggtaagtaaacagagtctgattagttctttctttcattctggcttgccttcaaatgttttacagAGCTCAGTCCTTGCCTTGGATGATTCAGCATTAGATGTTGATCAAGTTGATAACCTCATAAAGTTCTGTCCAACAAAAGAAGAGATTGAACTACTCAAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv04s0008g06530.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os02g55150.1 (Oryza sativa), 3'ss of exon 3
-cttgtgtctgttcagcaattctagtcccagacacgtggtaagta--aacagagtctgattagttctttctttcattctggcttgccttcaaatgttttacagAGCTCAGTCCTTGCCTTGGATGATTCAGCATTAGATGTTGATCAAGTTGATAACCTCATAAAGTTCTGTCCAACAAAAGAAGAGATTGAACTACTCAAG
| || | | || | | || ||| | | | | | |||| ||||| | | | | | |||| |||| |||||| ||||| | || ||||| | |||| ||||||||| ||| | || ||||||||||||||||| || ||||| || |||||||||||
attagttacctattgttgcaactgttactgagcataaagtatttggcagctgtactgaactagtggtttctgttgataatagtggttcct---tttttttcagAACTCAGTGCTTGCACTTGACGATTCCATTGTTGATGGTGATCAAGTAGATTATCTAATAAAGTTCTGTCCAACTAAGGAAGAAATGGAACTACTCAAA
upper sequence: Vv04s0008g06530.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA17G33930.1 (Glycine max), 3'ss of exon 6
--cttgtgtctgttcagcaattctagtcccagacacgtggtaagtaaacagagtctgattagttctttctttcattctggcttgccttcaaatgttttacagAGCTCAGTCCTTGCCTTGGATGATTCAGCATTAGATGTTGATCAAGTTGATAACCTCATAAAGTTCTGTCCAACAAAAGAAGAGATTGAACTACTCAAG
|| | |||| | || || | | || | ||| | | || | || ||||| ||| | ||| || ||| | | || ||||| ||||||||||||| ||| ||||||||||||||||| ||||||||||| |||| |||||| ||||||||||| ||| | || |||
aattttaaaccattcaattagtc-agaaaggaatgtctc-caatcgcagagaaacatgccaatttataattgtattctcatgtgctaatcattgtctttcagTGTGCTGTGCTTGCATTGGATGATTCAGTATTGGATGTTGATCAAGTTGAGAACCTCATAAAATTCTCTCCAACCAAAGAAGAGATGGAAATGCTGAAG
upper sequence: Vv04s0008g06530.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AT2G25050.2 (Arabidopsis thaliana), 3'ss of exon 6
-----------------------------------cttgtgtctgttcagcaattctagtcccagacacgtggtaagtaaacag---agtctgattagttctttct-------------ttcattctggcttgccttca-aatgttt---tacagAGCTCAGTCCTTGCCTTGGATGATTCAGCATTAGATGTTGATCAAGTTGATAACCTCATAAAGTTCTGTCCAACAAAAGAAGAGATTGAACTACTCAAG
|| || || | | || | | || |||| ||| | || | |||| | |||| | || | | ||| ||| | ||| ||| ||||||| || || ||||| |||||||| |||| ||||||||||||||||||| || || |||||||| ||||||||||||||||| ||| | ||||||
gtacgcacacattccttttgcaagatattgctttgctagttcttgacttgttctcttaagctctactacttggttagtgcaaagttcactctgctctcatcttgttatgcaagagctgcttaaaattttcttaacttaataatctttggttacagAGTTCTGTTCTTGCTTTGGATGAGTCAGTGATAGATGTTGATCAAGTTGACAATCTAATAAAGTTTTGTCCAACAAAAGAAGAAGCAGAATTGCTCAAG
upper sequence: Vv04s0008g06530.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AT3G32400.1 (Arabidopsis thaliana), 3'ss of exon 5
---------------------------------cttgtgtctgttcagcaattctagtcccagacacgtggtaagtaaacagagtctgattagttctt-tctt-tcattctggcttgccttcaaatgtt--------------------ttacagAGCTCAGTCCTTGCCTTGGATGATTCAGCATTAGATGTTGATCAAGTTGATAACCTCATAAAGTTCTGTCCAACAAAAGAAGAGATTGAACTACTCAAG
|| || || | | || | | || |||| ||| || ||| | | |||| |||| | || | | ||| |||| || |||||||| || || ||||| |||||||| |||| ||||||||||||||||||| || || |||||||| ||||||||||||||||| ||| | ||||||
gtacacacattctttttgcaagatatgtctttgctagttccttacttgttctcttaagctctacaacttggttagtg--caaagtttactctactcttatcttgttatgcaagagctgcttaaaattttcttaacttattaatctttggttacagAGTTCTGTTCTTGCTTTGGATGAGTCAGTGATAGATGTTGATCAAGTTGACAATCTAATAAAGTTTTGTCCAACAAAAGAAGAAGCAGAATTGCTCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acagagtctgattagttctttctttcattctggcttgccttcaaatgttttacagAGCTCAGTCCTTGCCTTGGATGATTCAGCATTAGATGTTGATCAAGTTGATAACCTCATAAAGTTCTGTCCAACAAAAGAAGAGATTGAACTACTCAAG
gtctgat putative branch site (score: 4)
aaatgtttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cttgtgtctgttcagcaattctagtcccagacacgtggtaagtaaacagagtctgattagttctttctttcattctggcttgccttcaaatgttttacagAGCTCAGTCCTTGCCTTGGATGATTCAGCATTAGATGTTGATCAAGTTGATAACCTCATAAAGTTCTGTCCAACAAAAGAAGAGATTGAACTACTCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - tgtctgt
- - - - - -tcagcaa
- - - - - - - - - - - - -cccagac
- - - - - - - - - - - - - - - - - - - - - -aaacaga