Sequence
atgc intronic sequence ATGC exonic sequence...ttagattgacaatttgataattatttcattcattttaactaaatatttcaaaaaaattatttataagattttgaaagtcaatttctaagtcaatttgcagAAGAAGAAAATGATCCTGATAGGAAGCCAACTAGAGAGAACATGAGAAGGGCATTGTATTGGCTTGTACAAGGCTGTCAACCTGGAGACTCCCTAGTGTT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv16s0013g00210.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G155422_T01 (Zea mays), 3'ss of exon 1
-ttagattgacaatttgataattatttcattcattttaactaaatatttcaaaaaaattatttataagattttgaaagtcaa---tttctaagtcaat-ttgcagAAGAAGAAAATGATCCTGATAGGAAGCCAACTAGAGAGAACATGAGAAGGGCATTGTATTGGCTTGTACAAGGCTGTCAACCTGGAGACTCCCTAGTGTT
|| || || | | | | | || | |||| | | | || || || | | | ||| || || ||| || | ||||||||||| ||| || || | | | ||||| | | ||||| | | ||| ||||||||||||| ||||| ||||||||||||||||| | |||||
ttttgaaacgttatgtactgagtgtagcaatttttttgataatgtgttgttt-----ctacttttgaaccctaaaaaagtaaacacttttaatacattcttgcagAAGAACAAACCGACCCCTACAAAATCCCAACAAAGCATAACATAGGGATGGCCATGTATTGGCTTGTGCAAGGTTGTCAACCTGGAGACTCATTGGTGTT
upper sequence: Vv16s0013g00210.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G035928_T01 (Zea mays), 3'ss of exon 1
ttagattgacaatttgataattatttcattcattttaactaaatatttcaaaaaaattatttataagattttgaaagtcaatt---tctaagtcaatt--tgcagAAGAAGAAAATGATCCTGATAGGAAGCCAACTAGAGAGAACATGAGAAGGGCATTGTATTGGCTTGTACAAGGCTGTCAACCTGGAGACTCCCTAGTGTT
| |||| || || || || | | | | ||| | || | | | | |||| | || | | | ||| |||||||||| ||| || || | | | ||||| | | ||||| || | ||| ||||||||||||| ||||| |||||||||||||| || | |||||
--attttga-aactttatg--taccaagtgtaagtgcttttgataatgtggcgtttctactcttgaaccctagaaaattaaacacatttggttacattcttgcagAAGAACAAACGGACCCCTACAAAATCCCAACAAAGCATAACATAAGGATGGCCATGTATTGGCTTGTGCAAGGTTGTCAACCTGGAGATTCATTGGTGTT
upper sequence: Vv16s0013g00210.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA01G10880.2 (Glycine max), 3'ss of exon 1
ttagattgacaatttgataattatttcat-tcattttaactaaatatttcaaaaaaattatttataagattt--tgaaagtcaatttctaagt--caatttgcagAAGAAGAAAATGATCCTGATAGGAAG---CCAACTAGAGAGAACATGAGAAGGGCATTGTATTGGCTTGTACAAGGCTGTCAACCTGGAGACTCCCTAGTGTT
| || || | || |||||| || | ||| | | | || ||| | || | | || | | | ||| | | | | ||| ||||||||||||| || | || || ||||| | | ||||| || | |||| |||||||||||| |||||| |||||||||||||||||||| ||
--atatggaagactt---aattatgctatgctacttttgttggaaaaaaaaagaaattcataaagcatatatactagtactcatcatttgaatttcaaaatgcagAAGAAGAAGATCCCCATGGCCCCAAATTTCCAACCAAGCACAACATCAGGATGGCAATGTATTGGCTTGCACAAGGATGTCAACCTGGAGACTCCCTGGT---
upper sequence: Vv16s0013g00210.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA08G45470.1 (Glycine max), 3'ss of exon 1
ttagattgacaatttgataattatttcat-tcattttaactaaatatttcaaaaaaattatttataagattt--tgaaagtcaatttctaagt--caatttgcagAAGAAGAAAATGATCCTGATAGGAAG---CCAACTAGAGAGAACATGAGAAGGGCATTGTATTGGCTTGTACAAGGCTGTCAACCTGGAGACTCCCTAGTGTT
||| | | ||||||| || | ||| | || | || ||| | || | | || | | | ||| | | | | ||| ||||||||||||| || | || || ||||| | | ||||| || | |||| |||||||||||| |||||| |||||||||||||||||||| ||
---atttggaagact--taattatgctatgctacttttgttgaaaaaaaaaagaaattcataaagcatatatactagtactcatcatttgaatttcaaaatgcagAAGAAGAAGATCCCCATGGCCCCAAATTTCCAACGAAGCACAACATCAGGATGGCAATGTATTGGCTTGCACAAGGATGTCAACCTGGAGACTCCCTGGT--- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttcaaaaaaattatttataagattttgaaagtcaatttctaagtcaatttgcagAAGAAGAAAATGATCCTGATAGGAAGCCAACTAGAGAGAACATGAGAAGGGCATTGTATTGGCTTGTACAAGGCTGTCAACCTGGAGACTCCCTAGTGTT
aaaaaattatttataa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttagattgacaatttgataattatttcattcattttaactaaatatttcaaaaaaattatttataagattttgaaagtcaatttctaagtcaatttgcagAAGAAGAAAATGATCCTGATAGGAAGCCAACTAGAGAGAACATGAGAAGGGCATTGTATTGGCTTGTACAAGGCTGTCAACCTGGAGACTCCCTAGTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - cattcat
- - - - - - - - - - - - - - - - - - aactaaa
- - - - - - - - - - - - - - - - - - - - - - - - -aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaagtcaa