Sequence
atgc intronic sequence ATGC exonic sequence...attagtagaacagcatttatgttcttgacattgttatactgtctactagttctgtttgatgcctctattgatttgtcgtacatgtctccctatgcgccagGAAATTTTTGTTCAGACAAGAAACCAGCTGCTGTAAACTGGATTGAAGGGCGTGGTAAGTCTGTGGTTTGTGAGGCAGTCATCAAGGAGGATGTGGTAAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv18s0122g00610.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA20G05530.1 (Glycine max), 3'ss of exon 2
attagtagaacagcatttatgttcttgacattgttatactgtct-actagttctgtt-tgatgcctctattgatttgtcgtacatgtct-ccctatgcgccagGAAATTTTTGTTCAGACAAGAAACCAGCTGCTGTAAACTGGATTGAAGGGCGTGGTAAGTCTGTGGTTTGTGAGGCAGTCATCAAGGAGGATGTGGTAAG
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---atacaagctgggatgctgaaattatatttgctgggaaatttgacttgaaatgtgatgattaattgaccaatatgtattgaatattgattcaattcttcagGAAATTACTGTTCAGACAAGAAACCTGCTGCAGTAAATTGGATTGAGGGACGTGGGAAGTCAGTGGTTTGTGAAGCAATTATCAAAGATGATGTGGTGAA
upper sequence: Vv18s0122g00610.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA02G44070.1 (Glycine max), 3'ss of exon 2
-attagtagaac-agcatttatgttcttgacattgttatactgtct-actagttctgtttgatgcctctattgatttgtcgtacatgtctccctatgcgccagGAAATTTTTGTTCAGACAAGAAACCAGCTGCTGTAAACTGGATTGAAGGGCGTGGTAAGTCTGTGGTTTGTGAGGCAGTCATCAAGGAGGATGTGGTAAG
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gtttatttgatttgatgcctataatcagggcatgctgaaattgttttattgggaggattagaccgaaatgtgatggttttgtac-tgacttc--atcctttagGAAATTATTGTTCGGACAAGAAACCTGCTGCAGTGAATTGGATCGAGGGACGTGGGAAATCAGTTGTTTGTGAAGCAATCATCAAAGAAGAAGTGGTGCA
upper sequence: Vv18s0122g00610.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA14G05020.1 (Glycine max), 3'ss of exon 2
attagtagaacagcatttatgttcttgacattgttatactgtct-actagttctgtttgatgcctctattgatttgtcgtacatgtct---ccctatgcgccagGAAATTTTTGTTCAGACAAGAAACCAGCTGCTGTAAACTGGATTGAAGGGCGTGGTAAGTCTGTGGTTTGTGAGGCAGTCATCAAGGAGGATGTGGTAAG
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---tttgatttgatgcctataatcaggacatgctgaaattgttttaatgggaatatt-aattagactgaaaatttgatggttatctactgacttgatcctttagGAAATTATTGTTCGGACAAGAAACCTGCTGCAGTAAATTGGATCGAGGGACGTGGGAAATCAGTTGTTTGTGAAGCAATTATCAAAGAAGAAGTGGTGCA
upper sequence: Vv18s0122g00610.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: PP1S139_2V6.1 (Physcomitrella patens), 3'ss of exon 2
attagtagaacagcatttatgttcttgacattgttatactgtctactagttc---tgtttgatgcctctattgatttgtcgtacat-------gtctccctatgcgccagGAAATTTTTGTTCAGACAAGAAACCAGCTGCTGTAAACTGGATTGAAGGGCGTGGTAAGTCTGTGGTTTGTGAGGCAGTCATCAAGGAGGATGTGGTAAG
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gtttgca--acatgaccca-gttgttggtccttcgtttcagttcattttttcgcttgtctagcgcttgtttagctgtacagtatactcacgtagtctgtacatgtgc-agGTAACTTCTGTGCGGACAAGAAACCAACAGCTGTAAACTGGATTGATGGTCGTGGAAAGTCTGTCGTTTGTGAGGCAATTTTGAAAGGGGACGTCGTACG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctagttctgtttgatgcctctattgatttgtcgtacatgtctccctatgcgccagGAAATTTTTGTTCAGACAAGAAACCAGCTGCTGTAAACTGGATTGAAGGGCGTGGTAAGTCTGTGGTTTGTGAGGCAGTCATCAAGGAGGATGTGGTAAG
tattgat putative branch site (score: 3)
tgtctccct putative PPT
tattgattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
attagtagaacagcatttatgttcttgacattgttatactgtctactagttctgtttgatgcctctattgatttgtcgtacatgtctccctatgcgccagGAAATTTTTGTTCAGACAAGAAACCAGCTGCTGTAAACTGGATTGAAGGGCGTGGTAAGTCTGTGGTTTGTGAGGCAGTCATCAAGGAGGATGTGGTAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - cagcatt
- - - - - - - - - - - - - - - - - - tactgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcctct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acatgtc