Sequence
atgc intronic sequence ATGC exonic sequence...tgtttgtttttgcttaaatgatgttatatatttgatgctgagttttatagtggttagtggtaagtggagattaatcgcgtggatggttctagtgtttcagGTGTGCAAGTTTGGATGGAGATGCTGATCGTCTTGTATATTTCCTTGTGCTACCAAAAGACAACAAGATTGATCTTGTTGATGGGGACAAGATATTGTCT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv02s0012g00620.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os07g09720.1 (Oryza sativa), 3'ss of exon 4
tgtttgtttttgcttaaatgatgttatatatttgatgctgagttttatagtggttagtggtaagtggagattaatcgcgtggatggttctagtgtttcagGTGTGCAAGTTTGGATGGAGATGCTGATCGTCTTGTATATTTCC---TTGTGCTACCAAAAGACAACAAGATTGATCTTGTTGATGGGGACAAGATATTGTCT
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-----------------gtga-gtcagttaattgctccttaaatttctacttgtcagttgtcactg-atcttacctggccattctgatctaac-tttcagGTGTGCAAGTTTTGATGGCGACGCTGACCGGCTTGTTTATTTCCGTATCGTATCCTCTAGTGACACTAGGATTGATCTCGTTGATGGTGACAAGATATTA---
upper sequence: Vv02s0012g00620.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G166597_T01 (Zea mays), 3'ss of exon 5
tgtttgtttttgcttaaatgatgttatatatttgatgctgagttttatagtggttagtggtaagtggagattaatcgcgtggatggttctagtgtttcagGTGTGCAAGTTTGGATGGAGATGCTGATCGTCTTGTATATTTCCTTGTGCTACCA---AAAGACAACAAGATTGATCTTGTTGATGGGGACAAGATATTGTCT
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-----gtgagacaatcggtagttgctcatgcttgatgcttgcctatctttatttttttagtcagcttaccattttc----------tcctagcattttagGTGTGCAAGTTTGGATGGTGATGCTGATCGACTCGTCTACTTCCGGTTGTCATCAGCTAGTGACAATAGGGTTGATCTTGTTGATGGAGATAAGATACTA---
upper sequence: Vv02s0012g00620.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA01G40950.1 (Glycine max), 3'ss of exon 6
tgtttgtttt--tgcttaaatgatgttatatatttgatgctgagttttatagtggttagtggtaagtggagattaatcgcgtggatggttctagtgtttcagGTGTGCAAGTTTGGATGGAGATGCTGATCGTCTTGTATATTTCCTTGTGCTACCAAAAGACAA---CAAGATTGATCTTGTTGATGGGGACAAGATATTGTCT
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-gttagccctaccattttagtatatgtattcttttagtgttg--ttatattgatgttctttatta-tggtctttactaatggagctagttctagT-TTGTAGGTGTGTTAGTTTGGATGGAGATGCTGATCGGCTTGTTTATTTTACTGTGCCACCTGAAAGCAGTGGTAGGATTGACCTTGTTGATGGGGACAA----------
upper sequence: Vv02s0012g00620.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA20G22760.1 (Glycine max), 3'ss of exon 4
--tgtttgtttt--tgcttaaatgatgttatatatttgatgctgagttttatagtggttagtggtaagtggagattaatcgcgtggatggttctagtgtttcagGTGTGCAAGTTTGGATGGAGATGCTGATCGTCTTGTATATTTCCTTGTGCTACCAAAAGACA---ACAAGATTGATCTTGTTGATGGGGACAAGATATTGTCT
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taagttagccctaccattttagtatatgtattcttttagtgttg--ttatattggtgttctttatta-tggtctttactaatggagctagttctagt-ttgtagGTGTGTTAGTTTGGATGGAGATGCTGATCGGCTTGTTTATTTTATTGTGCCACCTGAAAGCAGTGGTAGGATTGACCTTGTTGATGGGGACAAGATACTA---
upper sequence: Vv02s0012g00620.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: PP1S211_20V6.1 (Physcomitrella patens), 3'ss of exon 5
tgtttgtttttgcttaaatgatgttatat-atttgatgctgagttttatagtggttagtggtaa----gtggagattaatcgcgtggatggttctagtgtttcagGTGTGCAAGTTTGGATGGAGATGCTGATCGTCTTGTATATTTCCTTGTGCTACCAAAAG-ACAACAAGATTGATCTTGTTGATGGGGACAAGATATTGTCT
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---ttcttataatttggttgatactttttcagttcatagcatgttaaaca-tgactcgtcttgtttttgtgttgctaagacctcattttggattttat-ctccagGTGTGCGAGTCTTGATGGTGATGCTGATCGTCTTGTATATTTTTACATGTCTTCAATGTCGCAAACGGATCAAATTTCTCCCTCTTTACAAT-TGCTGGAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatagtggttagtggtaagtggagattaatcgcgtggatggttctagtgtttcagGTGTGCAAGTTTGGATGGAGATGCTGATCGTCTTGTATATTTCCTTGTGCTACCAAAAGACAACAAGATTGATCTTGTTGATGGGGACAAGATATTGTCT
gattaat putative branch site (score: 3)
agattaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgtttgtttttgcttaaatgatgttatatatttgatgctgagttttatagtggttagtggtaagtggagattaatcgcgtggatggttctagtgtttcagGTGTGCAAGTTTGGATGGAGATGCTGATCGTCTTGTATATTTCCTTGTGCTACCAAAAGACAACAAGATTGATCTTGTTGATGGGGACAAGATATTGTCT
- - - - - - - - - - - - - - - - -gatgctg
- - - - - - - - - - - - - - - - - - - - - - - - - tggttag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggatgg