Sequence
atgc intronic sequence ATGC exonic sequence...tttgagttgtgcttaaaaagacattgtgcaaaggatagttatgtttctatatgtttgatggttatgtcaagtgttaagaatctcaattagatgtgtgcagGCTGTTATTGTTCGACCTCTATCTGCGGTAAGCTCCCTTGTTCGATTTGCCGAGGAGCCCCAGATGTTTGCAATTGAATTCAATGATGGATGCCCTATTC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv11s0016g04420.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os10g42439.1 (Oryza sativa), 3'ss of exon 4
-------------------------------------tttgagttgtgcttaaaaagacattgtgcaaaggatagttatgtttctatatgtttgatggttatgtcaagtgttaagaatctcaattagatgtgtgcagGCTGTTATTGTTCGACCTCTATCTGCGGTAAGCTCCCTTGTTCGATTTGCCGAGGAGCCCCAGATGTTTGCAATTGAATTCAATGATGGATGCCCTATTC
| || | | || ||||| | | | | ||| | | | | | || | | | ||| ||| | | | |||||| | |||||||||||||| || | ||||| ||||||| |||||||| || || || |||||||||||| | |||||||||||||| ||||| ||||
gtaagtcttttgttgcaccctctacatggttgtctcctctggagtttcttttgcaagaccgcttctccttccttgctccctttatctttagcatgttagggttctaacttctttgc-tctgaatattttcttttcagGCTATCATTGTTCGACCTCTCTCAACAGTAAGTGCCCTTGTGCGATTTGCAGAAGAACCGCAGATGTTTGCATTCGAATTCAATGATGGTTGCCCGATTC
upper sequence: Vv11s0016g04420.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G367023_T01 (Zea mays), 3'ss of exon 4
--tttgagttgtgcttaaaaagacattgtgcaaaggatagttatgtttctatatgtttgatggttatgtcaagtgttaagaatctcaattagatgtgt--gcagGCTGTTATTGTTCGACCTCTATCTGCGGTAAGCTCCCTTGTTCGATTTGCCGAGGAGCCCCAGATGTTTGCAATTGAATTCAATGATGGATGCCCTATTC
| | || |||| || | | | || | | | | | ||| | |||| | || ||| | | | | || | | ||||||| ||||| ||||| || || || ||||| | ||||||||||||| || ||||| |||||||||||| |||||||||||||||| ||||| ||||
aagataatcagtccttagggtagaat-atatataagagactca-gctaatatgggccatatgg--gccttaacacttacttgtttgcactgaatttctttccagGCTGCCATTGTACGACCACTCTCAGCAGTAAGTGCTTTTGTTCGATTTGCTGAAGAGCCACAGATGTTTGCATTTGAATTCAATGATGGCTGCCCAATTC
upper sequence: Vv11s0016g04420.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G049288_T01 (Zea mays), 3'ss of exon 4
tttgagttgtgcttaaaaagacattgtgcaaaggatagttatgtttctatatgtttgatggttatgtcaagtgttaagaatctcaattagatgtgtgcagGCTGTTATTGTTCGACCTCTATCTGCGGTAAGCTCCCTTGTTCGATTTGCCGAGGAGCCCCAGATGTTTGCAATTGAATTCAATGATGGATGCCCTATTC
|| | | | | | |||| | || |||| | | | |||||||| || || ||||| || || || ||||| | ||||||||||||| || || || ||||| |||||| |||||||||||||||| ||||| ||||
---------------------------------------------------------ataggt-tcttacttgtttgca--ctgaatt---tctttccagGCTGTCATAGTACGACCACTCTCAGCAGTAAGTGCTCTTGTTCGATTTGTAGAAGAACCACAGATATTTGCATTTGAATTCAATGATGGCTGCCCAATTC
upper sequence: Vv11s0016g04420.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA17G12950.1 (Glycine max), 3'ss of exon 4
tttgagttgtgcttaa-aaagacat-tgtgcaaaggatagttatgttt---ctatatgtttgatggttatgtcaagtgttaagaatctcaattagatgtgtgcagGCTGTTATTGTTCGACCTCTATCTGCGGTAAGCTCCCTTGTTCGATTTGCCGAGGAGCCCCAGATGTTTGCAATTGAATTCAATGATGGATGCCCTATTC
|| |||| | || |||| | | ||| | |||| || | |||||||||||||||| ||||| | | |||||||||||||||||||| |||||| ||| ||||| | ||||| | |||||||| ||||| || |||||||||||||||||||||||||| | |||||||||||| || |
-----atttcatttaatgcatttatatgtgtctatgctagctgagttttacttagaatcagaggggttatgtcaagtgttgagaatttttactagatgtgtgcagGCTGTTACTGTTCGTCCTTTATCTTCAGTAAGTGCTCTTGTTCGGTTTGCTGAAGAGCCCCAGATGTTTGCAATTGAATTTAGTGATGGATGCCCCATCC
upper sequence: Vv11s0016g04420.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA05G08040.1 (Glycine max), 3'ss of exon 4
tttgagttgtgcttaaaaagacattgtgcaaaggatagttatgttt---ctatatgtttgatggttatgtcaagtgttaagaatctcaattagatgtgtgcagGCTGTTATTGTTCGACCTCTATCTGCGGTAAGCTCCCTTGTTCGATTTGCCGAGGAGCCCCAGATGTTTGCAATTGAATTCAATGATGGATGCCCTATTC
| || | |||| | || | || || | |||| ||| | ||||||||||||||| ||||| | | ||||||| |||||||||||| |||||| || ||||| | |||| | |||||||| ||||| || |||||||||||||||||||||||||| | |||||||||||| || |
---aatttcttattaatgcatttatatgtctatgaaagctgagttttactcataatgagaagtgttatgtcaagtgttgagaatttttactagatgtttgcagGCTGTTACTGTTCGTCCGTTATCTTCAGTAACTGCTCTTGTTCGGTTTGCTGAAGAGCCCCAGATGTTTGCAATTGAATTTAGTGATGGATGCCCCATCC
upper sequence: Vv11s0016g04420.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: PP1S60_221V6.1 (Physcomitrella patens), 3'ss of exon 4
tttgagttgtgcttaaaaagacattgtgcaaaggatagttatgtttctatatgtttgatggttatgtcaagtgttaagaatctcaattagatgtgtg-cagGCTGTTATTGTTCGACCTCTATCTGCGGTAAGCTCCCTTGTTCGATTTGCCGAGGAGCCCCAGATGTTTGCAATTGAATTCAATGATGGATGCCCTATTC
|| |||| | || | |||| | || | | | | | | | | | | ||| | | | ||| ||||| || ||||| ||| || |||||||||| |||||||| ||||| ||||| ||||| |||||||| ||||| ||||||||||| |||||| |||
ccaaagaaaaaagaaaaagaaaataaagaaaagacaaaatagaaagaaagaaaatcagctcctgcatttc-tctggaaactaacaaatggttctgtttcagGCGGTCATTGTCCGATCTTTATCTGCGGTGGCTGGTCTTGTTCGGTTTGCTGAGGAACCCCAAATGTTTGCGATTGACTTCAATGATGGTTGCCCTCTTC
upper sequence: Vv11s0016g04420.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: EFJ35138 (Selaginella moellendorffii), 3'ss of exon 5
tttgagttgtgcttaaaaagacatt---gtgcaaaggatagttatgtttctat--atgtttga-tggttatgt-caagtgttaagaa-tctcaattagatgt--gtgcagGCTGTTATTGTTCGACCTCTATCTGCGGTAAGCTCCCTTGTTCGATTTGCCGAGGAGCCCCAGATGTTTGCAATTGAATTCAATGATGGATGCCCTATTC
| || || | |||| | | | | | || | || | | ||| || | | | ||||||| | || | | || | ||||| || | || ||| |||||||| | | | | || ||||||||||| |||||||||||||||||||| ||||| || |||||||||||| | |
---gtatttctctacagtttgcattcaagcgtgattgtttttttagctttcttcaaaacttgcctgagtgcatgctggtgttaacaggtcattgatggttgatggaacagGCAGTGAGTGGTCGGCCTCTATCGTCAGCAGCAGCTCTCGTTCGATTTGCTGAGGAGCCCCAGATGTTTGCTATTGAGTTTGGTGATGGATGCCCAGTCC
upper sequence: Vv11s0016g04420.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: EFJ24089 (Selaginella moellendorffii), 3'ss of exon 5
tttgagttgtgcttaaaaagacatt---gtgcaaaggatagttatgtttctatat-gtttga-tggttatgt-caagtgttaagaa-tctcaattagatgt--gtgcagGCTGTTATTGTTCGACCTCTATCTGCGGTAAGCTCCCTTGTTCGATTTGCCGAGGAGCCCCAGATGTTTGCAATTGAATTCAATGATGGATGCCCTATTC
| || || | |||| | | | | | ||| ||||| | | ||| || | | | |||||| | || | | || | ||||| || | || ||| |||||||| | ||| | || ||||||||||| |||||||||||||||||||| ||||| || |||||||||||| | |
---gtatttctctacagtttgcattcaagcgtgattgttttttagctttcttcaaagcttgcctgagtgcatgctgttgttaacaggtcattgatggttgatggaacagGCAGTGAGTGGTCGGCCTCTATCGTCAGTAGCAGCTCTCGTTCGATTTGCTGAGGAGCCCCAGATGTTTGCTATTGAGTTTGGTGATGGATGCCCAGTCC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctatatgtttgatggttatgtcaagtgttaagaatctcaattagatgtgtgcagGCTGTTATTGTTCGACCTCTATCTGCGGTAAGCTCCCTTGTTCGATTTGCCGAGGAGCCCCAGATGTTTGCAATTGAATTCAATGATGGATGCCCTATTC
gtttgat putative branch site (score: 5)
ttaagaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttgagttgtgcttaaaaagacattgtgcaaaggatagttatgtttctatatgtttgatggttatgtcaagtgttaagaatctcaattagatgtgtgcagGCTGTTATTGTTCGACCTCTATCTGCGGTAAGCTCCCTTGTTCGATTTGCCGAGGAGCCCCAGATGTTTGCAATTGAATTCAATGATGGATGCCCTATTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - aaaaaga
- - - - - - - - - - - - - - caaagga
- - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatggt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caagtgt