Sequence
atgc intronic sequence ATGC exonic sequence...tcttcactataactgttgttatttggggctgaccatttttctttttctatgtcacgatatttctctattgatgtcttattaactgacttatctgtttcagTCCCAACTGGAGGAAATTGCACCTACATGGATGAATATTTCTTTGAGAATGAAAGATGATCCAGAGACAGATAAAGCTTTTGGATGGGTGCTAGAAAT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv06s0009g03360.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os05g32060.1 (Oryza sativa), 3'ss of exon 3
---------------------------------------------------------------------------------tcttcactataactgttgttatttggggctgac-------catttt----tctttttctatgtcacgat--atttctctattgatgtcttattaactgactt---atctgtttcagTCCCAACTGGAGGAAATTGCACCTACATGGATGAATATTTCTTTGAGAATGAAAGATGATCCAGAGACAGATAAAGCTTTTGGATGGGTGCTAGAAAT
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gtatctctcatctcgacgcatgattaataggatgcttaggtccggctataggagctgtcaagaactcaagatagcactgtctgcccaaactagttcttttcagttccgcataaaaaacatacatttaagaacattgtgcaatgccatagttcaatactgtttcaatgcattcgtga-tgccttcaaaacatctccagGCCCAGCTTGAGAAGATTGCTCCAACTTGGATGAATATTTCGTTGAAAATGAAAGAGGATGTGGAGACAGACAAAGCTTTTGGATGGGTCTTGGAAAT
upper sequence: Vv06s0009g03360.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os01g16600.1 (Oryza sativa), 3'ss of exon 3
------------------------------------------------------------------------tcttcactataactgt-tgttatttggggctgaccatttttctttttctatgtcacgatatttctctattgatgtcttattaactgacttatctgtttcagTCCCAACTGGAGGAAATTGCACCTACATGGATGAATATTTCTTTGAGAATGAAAGATGATCCAGAGACAGATAAAGCTTTTGGATGGGTGCTAGAAAT
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gtaacacatattgcagaattgacgtggtataccttgaagtctcatgcatgaggagtatttccttggattttatttttacattacttacatgccagttgctagttattaatgttttgaattgatgagcttcaatttttaactctatcccttatcatctgaggaaact--tttagATACAACTTGAGAAGATTGCCCCTACATGGATGAATGTATCGATTCAAATGAAAGAAGATCAGGAGACAGATAAAGCTTTTGGATGGGTCTTGGAAAT
upper sequence: Vv06s0009g03360.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G035595_T02 (Zea mays), 3'ss of exon 3
------------------------------------------------------------------------tcttcactataactgttgttatttggggc-tgaccatttttctttttctatgtcacgatatttctctattgatgtcttattaactgacttatctgtttcagTCCCAACTGGAGGAAATTGCACCTACATGGATGAATATTTCTTTGAGAATGAAAGATGATCCAGAGACAGATAAAGCTTTTGGATGGGTGCTAGAAAT
|| | | || | ||| || | | || |||| ||| | ||| | | || || | || || | | |||| | || ||| | ||||| || |||||||||||| | || | ||||||||| ||| |||||||||||||| ||||||||||||| | |||||
gtattttcttgttgcacacttaacacccattcacctaagcatgttattgattttctgaccattcatttggtgcattagcattcacagcctttacttcgcttgttactatttcggtttagtaacttcataagacctcacttcacacaatttcttttcctgtgagagcttctcagACAATTCTTGAGAAGATTGCCCCCACATGGATGAATGTGTCAATTCAAATGAAAGAGGATGAAGAGACAGATAAAGTTTTTGGATGGGTGTTGGAAAT
upper sequence: Vv06s0009g03360.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA02G44810.1 (Glycine max), 3'ss of exon 5
------------------------------------------------------------------tcttcactataactgttgttatttggggctgaccatttttctttttctatgt-cacgatatttctctattgatgtcttattaactgacttatctgtttcagTCCCAACTGGAGGAAATTGCACCTACATGGATGAATATTTCTTTGAGAATGAAAGATGATCCAGAGACAGATAAAGCTTTTGGATGGGTGCTAGAAAT
| | | | |||||| | | | || || | |||| | || || ||||| | ||| | | | | | | ||||| |||||| |||||||||| || | |||||| | ||| |||| ||||||||||||||||||| |||||| ||||||||||||||||||||||| |||||
gtgaaatctcaatagtctgcatactgtgcttgattgattttagtagttatattgtgacccatatagctgtaattgttactgttatagctattatcagatttttgtgattttcccataagcaacatattctttcatttaaggcattgaattttctttatca---tcagTCTTTGATGGAGGAAATAGCTTCCACATGGGTAAATGTTTCATTGAGAATGAAAGATGATCAAGAGACTGATAAAGCTTTTGGATGGGTGCTTGAAAT
upper sequence: Vv06s0009g03360.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA14G03930.1 (Glycine max), 3'ss of exon 3
-----------------------------------------------------------------tcttcactataactgttgttatttggggctgaccatttttctttttctatgt-cacgatatttctctattgatgtcttattaactgacttatctgtttcagTCCCAACTGGAGGAAATTGCACCTACATGGATGAATATTTCTTTGAGAATGAAAGATGATCCAGAGACAGATAAAGCTTTTGGATGGGTGCTAGAAAT
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gtaagtctcaatagtttgcatactgtgcttgattgattatacctgttatactgtgacccatatagctgtaatggttactgttataactattatcagatttccgtgattttcccataagcaacatattctttcatttaaggcat-tgaattttcttaatcat--cagTCTTTGATGGAGGAAATAGCTCCAACATGGGTAAATATTTCATTGAGAATGAAAAATGATCCAGAGACTGATGAAACTTTTGGATGGGTGCTTGAAAT
upper sequence: Vv06s0009g03360.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA20G08020.1 (Glycine max), 3'ss of exon 3
-----tcttcactataactgttgttatttggggctgaccatttttct--ttttcta--tgtcacgatatttctc-tattgatgtcttattaa----ctgacttatctgtttc---agTCCCAACTGGAGGAAATTGCACCTACATGGATGAATATTTCTTTGAGAATGAAAGATGATCCAGAGACAGATAAAGCTTTTGGATGGGTGCTAGAAAT
| |||| ||| | ||| | ||| |||| || | ||||| ||| | ||| | || | | ||| | || || ||| | || ||||| || |||||||| || || |||||| |||||||||| ||| ||||||||||||||| | || || || ||||||||||||| || |||||
gtcaattttcaacatacacat-gttgcc--agattgatttttttactaatattctaactgttatattataaagcataatagccttccattgagactttggtttttctttatcatcagTCCTTGCTAGAGGAAATAGCTCCCACATGGGTGAATATTTCCTTGCAAATGAAAGATGATCCGGCAACTGACGAAACTTTTGGATGGGTACTTGAAAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctatgtcacgatatttctctattgatgtcttattaactgacttatctgtttcagTCCCAACTGGAGGAAATTGCACCTACATGGATGAATATTTCTTTGAGAATGAAAGATGATCCAGAGACAGATAAAGCTTTTGGATGGGTGCTAGAAAT
tctgtttc CT-rich tract
tcttattaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcttcactataactgttgttatttggggctgaccatttttctttttctatgtcacgatatttctctattgatgtcttattaactgacttatctgtttcagTCCCAACTGGAGGAAATTGCACCTACATGGATGAATATTTCTTTGAGAATGAAAGATGATCCAGAGACAGATAAAGCTTTTGGATGGGTGCTAGAAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
tcttcac
- - - - - - ctgttgt
- - - - - - - - - - - - - - ctgacca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatgtc