Sequence
atgc intronic sequence ATGC exonic sequence...tcatgattcagtgtccatcatattgacaatagttaaccatactctaggtatgatacctgtgatctgactgtcattttcgtttttgctctttcattttcagTATACACCAGCAATAGATATATGGAGCATTGGATGCATCTTTGCAGAGCTTTTAACTGGAAAACCTCTCTTTCCTGGAAAAAATGTTGTTCACCAATTGG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv05s0020g02530.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os05g05160.1 (Oryza sativa), 3'ss of exon 4
-----tcatgattcagtgtccatc-atattgacaatagttaaccatactctaggtatgatacctgtgat-ctgactgtcattttcgtttttgctctttcattttcagTATACACCAGCAATAGATATATGGAGCATTGGATGCATCTTTGCAGAGCTTTTAACTGGAAAACCTCTCTTTCCTGGAAAAAATGTTGTTCACCAATTGG
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aagtgtacacatgtattctccttttattttttgcatgggcttctatgttt---gtccaatatccgaagcaccgatgaacataatgtgtttcattattttg----cagTATACACCAGCAATAGATATATGGAGTATTGGCTGCATATTTGCCGAGCTTTTAACCGGAAAACCTCTTTTCCCTGGGAAGAATGTGGTTCATCAACTTG
upper sequence: Vv05s0020g02530.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os11g17080.1 (Oryza sativa), 3'ss of exon 4
-tcatgattcagtgtcca--tcatattgacaatagttaaccatactctaggtatgatacctgtgatctgactgtcattttcgtttttgctctttcattttcagTATACACCAGCAATAGATATATGGAGCATTGGATGCATCTTTGCAGAGCTTTTAACTGGAAAACCTCTCTTTCCTGGAAAAAATGTTGTTCACCAATTGG
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gcaatgaaatgctgtctagttccagttgctggctatatttttctttgtacatataatgcctggagtat--cggtgaaccttatact-gttcaaattcttgcagTACACACCAGCAATAGATATATGGAGCATCGGTTGCATATTTGCAGAACTTTTAACAGGAAAACCTCTTTTCCCCGGGAAAAATGTGGTGCATCAACTTG
upper sequence: Vv05s0020g02530.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G017351_T01 (Zea mays), 3'ss of exon 3
tcatgattcagtgtccatcata---ttgacaatagttaaccatactctaggtatgatacctgtgatctgactgtcattttcgtttttgctctttcattttcagTATACACCAGCAATAGATATATGGAGCATTGGATGCATCTTTGCAGAGCTTTTAACTGGAAAACCTCTCTTTCCTGGAAAAAATGTTGTTCACCAATTGG
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-catgctcttttgttcataagaagcttcactcttgtataat-tgccttgtatagtttgttcgatatctgaggaatactgttgaacattgtgtttt-tttacagTATACACCAGCGATAGATATATGGAGTATTGGTTGTATATTTGCGGAACTATTAACTGGAAAACCGCTTTTCCCGGGGAAAAATGTGGTACATCAACTTG
upper sequence: Vv05s0020g02530.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G089484_T01 (Zea mays), 3'ss of exon 4
--tcatgattcagtgtcca-tcatattgacaatagttaaccatactctaggtatgatacctgtgatctgactgt-cattttcgtttttgctctttcattttcagTATACACCAGCAATAGATATATGGAGCATTGGATGCATCTTTGCAGAGCTTTTAACTGGAAAACCTCTCTTTCCTGGAAAAAATGTTGTTCACCAATTGG
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gattgttgcatatttccttctcacctgttccatggccctgtatagttt--gtgaaatatctggagcaccattgaacaaatatgtgttttttgttt--tttgtagTATACACCGGCGATAGATATATGGAGTATTGGCTGTATATTTGCAGAATTGTTAACTGGAAAACCTCTTTTCCCGGGGAAAAATGTGGTACATCAACTTG
upper sequence: Vv05s0020g02530.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA17G02220.1 (Glycine max), 3'ss of exon 4
tcatgattcagtgtccatcatattgacaatagttaaccatact--ctag-gtatgatacctgtgatctgactgtcattttcgtttttgctctttcattttcagTATACACCAGCAATAGATATATGGAGCATTGGATGCATCTTTGCAGAGCTTTTAACTGGAAAACCTCTCTTTCCTGGAAAAAATGTTGTTCACCAATTGG
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--atagtt-actgcttactttgtagtcaaataaaaaaaatggttgctagtgtttgtgaaatgaagatggataatcaatgttgttataatcttttttctttcagTATACCCCAGCTATAGACATATGGAGCATTGGCTGCATTTTTGCAGAACTTTTAACTGGAAAACCTCTTTTCCCAGGGAAGAATGTTGTCCATCAATTGG
upper sequence: Vv05s0020g02530.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA13G28120.1 (Glycine max), 3'ss of exon 4
----tcatgattcagtgtccatcatattgacaatagttaaccatactctaggtatgatacctgtgatctgactgtcattttcgtttttgctctttcatttt-cagTATACACCAGCAATAGATATATGGAGCATTGGATGCATCTTTGCAGAGCTTTTAACTGGAAAACCTCTCTTTCCTGGAAAAAATGTTGTTCACCAATTGG
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tggacaatgtttctatgc---ttctgtgtaccataatgatttattatcttatcccgg-acctg-gacttggtaaacatatttggtcataaacttttgtttttcagTATACACCAGCTATAGACATATGGAGCATTGGCTGCATTTTTGCAGAACTTTTGACGGGAAAACCTCTTTTCCCTGGGAAGAATGTTGTCCATCAACTAG
upper sequence: Vv05s0020g02530.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA15G10940.4 (Glycine max), 3'ss of exon 4
tcatgattcagtgtccatcatattgacaatagttaaccatact--ctaggtatgatacctgtgatctgactgtcattttcgtttttgctctttcatttt-cagTATACACCAGCAATAGATATATGGAGCATTGGATGCATCTTTGCAGAGCTTTTAACTGGAAAACCTCTCTTTCCTGGAAAAAATGTTGTTCACCAATTGG
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-tgaagttggacaatgcttctat--gcttctgtgtaccttaatgatttattatcttatcctggactttgtaaatatatttggtcataaacttttgtttttcagTATACACCAGCTATAGACATATGGAGCATTGGCTGCATTTTTGCTGAACTTTTGACCGGAAAACCTCTTTTCCCTGGGAAGAATGTTGTTCATCAACTAG
upper sequence: Vv05s0020g02530.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA07G38510.1 (Glycine max), 3'ss of exon 3
tcatgattcagtgtccatcatattgacaatagttaaccatact--ctag-gtatgatacctgtgatctgactgtcattttcgtttttgctctttcattttcagTATACACCAGCAATAGATATATGGAGCATTGGATGCATCTTTGCAGAGCTTTTAACTGGAAAACCTCTCTTTCCTGGAAAAAATGTTGTTCACCAATTGG
| || | | | | ||| | || || || || | |||| || || | || || ||| | | ||| | ||| ||||||||||| ||||| ||||| |||||||||||||| ||||| || ||||| |||||||||||||||||||| || || || || |||||||| || |||||||
-taggagttatttt--atccctctaaccatgcctattaatggttgctagtgtttgtgaaatgaagatggataatcaatgttgttataatcttttgtctttcagTATACCCCAGCTATAGACATATGGAGCATTGGCTGCATTTTCGCAGAACTTTTAACTGGAAAACCTCTTTTCCCAGGGAAGAATGTTGTCCATCAATTGG
upper sequence: Vv05s0020g02530.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT5G19010.1 (Arabidopsis thaliana), 3'ss of exon 4
-------------------------------------------tcatgattcagtgtccatcatattgacaatagttaaccatactctaggtatgatacctgtgatctgactgtcattttcgtttttgctctttcattttcagTATACACCAGCAATAGATATATGGAGCATTGGATGCATCTTTGCAGAGCTTTTAACTGGAAAACCTCTCTTTCCTGGAAAAAATGTTGTTCACCAATTGG
| | || | || | | |||| || | | | || | | | | | | || | ||||| || | | ||| | ||||||||||||| |||||||||||||||||||| || ||||| |||||||| || ||||| || |||||||| || || || |||||||| || || |||||||
gtgaccatgattttgtatatatactttcatcgaatgtttcaaattttcatagggaatctagtcagtagacactatagctctctcattcagattataaaattttatggtaacattttttttctttatctatgcttc-tgttcagTATACACCGGCAATAGATATATGGAGCATCGGGTGCATTTTTGCAGAACTCTTAACAGGGAAACCTCTTTTCCCCGGGAAAAATGTGGTCCATCAATTGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aggtatgatacctgtgatctgactgtcattttcgtttttgctctttcattttcagTATACACCAGCAATAGATATATGGAGCATTGGATGCATCTTTGCAGAGCTTTTAACTGGAAAACCTCTCTTTCCTGGAAAAAATGTTGTTCACCAATTGG
atctgac putative branch site (score: 3)
tcattttcgtttttgc putative PPT
tttcatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcatgattcagtgtccatcatattgacaatagttaaccatactctaggtatgatacctgtgatctgactgtcattttcgtttttgctctttcattttcagTATACACCAGCAATAGATATATGGAGCATTGGATGCATCTTTGCAGAGCTTTTAACTGGAAAACCTCTCTTTCCTGGAAAAAATGTTGTTCACCAATTGG
-catgatt
- - - - - - - ccatcat
- - - - - - - - - - - - - - - - - aaccata
- - - - - - - - - - - - - - - - - - - - - - - ggtatga
- - - - - - - - - - - - - - - - - - - - - - - - - - -tacctgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgactgt