Sequence
atgc intronic sequence ATGC exonic sequence...atttcctactgttttattatttttttatgcctcaaacatgagcaaatagtttataattgtttttccagcatcactgtgattatgaacattttaattgcagGCCCCAGGTAACAATTGCTACAGCAATCATATTTTGTCACCGTTTCTTCCTTCGTCAATCCCATGCAAAGAATGACAGAAGG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv19s0027g01670.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os12g30020.2 (Oryza sativa), 3'ss of exon 2
--atttcctactgttttattatttttttatgcctcaaacatgagcaaatagtttataattgtttttccagcatcactgtgattatgaacattttaattgcagGCCCCAGGTAACAATTGCTACAGCAATCATATTTTGTCACCGTTTCTTCCTTCGTCAATCCCATGCAAAGAATGACAGAAGG
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ggtcatgtgaatactacat-attgtttagtttttcttatttatg-gagtataatatcattctgtctacttccaatcaatgactgccttttgttctgtggtagGCCACAAGTCACTATTGCTACAGCTATTGTGTTCTGTCACCGTTTTTACCTTCGTCAGTCCCATGCAAAAAATGATAGACGA
upper sequence: Vv19s0027g01670.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G115670_T01 (Zea mays), 3'ss of exon 1
atttcctactgttttattatttttttatgcctcaaacatgagcaaatagtttataattgtttt--tccagcatcact--gtgattatgaacattttaattgcagGCCCCAGGTAACAATTGCTACAGCAATCATATTTTGTCACCGTTTCTTCCTTCGTCAATCCCATGCAAAGAATGACAGAAGG
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---tggaacttttttatgttttaaatggactgcat-tgtcatcaaatatgttggaagtcttttagctcatccttttctcatagtcattggttcgctgtttttagGCCCCAAGTGACGATTGCTACAGCTACGGTATTCTGTCACCGTTTTTTCCTTCGTCAATCCCATGCAAAGAATGATAGACGA
upper sequence: Vv19s0027g01670.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G377311_T01 (Zea mays), 3'ss of exon 2
atttcctactgttttattatttttttat--gcctcaaacatg----agcaaatagtttataattgtttttccag--catcactgtgattatgaacattttaattgcagGCCCCAGGTAACAATTGCTACAGCAATCATATTTTGTCACCGTTTCTTCCTTCGTCAATCCCATGCAAAGAATGACAGAAGG
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--------atatttaatggatcctgcattcacaccaagtttgtcaaagtaaatacttttcgctcatccttttatctcgtaaaatctaccttacctgtgctgtttttagGCCCCAAGTGACGATTGCCACAGCAATGGTATTCTGTCATCGTTTTTACCTTCGTCAATCCCTTGCAAAAAATGATAGACGA
upper sequence: Vv19s0027g01670.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA08G17960.1 (Glycine max), 3'ss of exon 1
--atttcctactgttttattatttttttatgcctcaaacatgagcaaatagtttataattgtttttccagcatcactgtgattatgaac-attttaattgcagGCCCCAGGTAACAATTGCTACAGCAATCATATTTTGTCACCGTTTCTTCCTTCGTCAATCCCATGCAAAGAATGACAGAAGG
||| || || | |||| | ||| | | |||| || || ||| | ||| | ||| ||| | || ||||||||| |||||||| ||||| || ||||| ||||||||||| || ||||| || || || |||||||||||||||||| | |||
ttgtttatctctattatcatattaaaattgataataaatgtcaatgaataccctaagcttcattt---atcatgatgttgacactgatttaattgtgttgcagGCCTCAGGTAACTATTGCAACTGCAATAATATTTTGTCATCGATTCTTTCTCCGGCAGTCCCATGCAAAGAATGACCGGAGG
upper sequence: Vv19s0027g01670.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA15G41040.1 (Glycine max), 3'ss of exon 1
atttcctactgttttattatttttttatgcctcaaacatgagcaaatagtttataattgtttttccagcatcactgtgattatgaac-attttaattgcagGCCCCAGGTAACAATTGCTACAGCAATCATATTTTGTCACCGTTTCTTCCTTCGTCAATCCCATGCAAAGAATGACAGAAGG
|| | || | |||| || || || | | | ||| ||| | | | || | | ||| | |||| || | || |||||| || |||||||| ||||| || ||||| ||||||||||| || ||||| || || || |||||||||||||||||||| |||
atgtttatctatattatcatattaaaattgataataaatgt-caatgaatacacttagcttcatttatcatgatgttgatgctgttttaattgtgttgcagACCTCAGGTAACTATTGCAACTGCAATAATATTTTGTCATCGATTCTTTCTCCGGCAGTCCCATGCAAAGAATGACAGGAGG
upper sequence: Vv19s0027g01670.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: EFJ37217 (Selaginella moellendorffii), 3'ss of exon 1
-------------atttcctactgttttattatttttttatgcctcaaacatgagcaaa-tagtttataattgtttttccagcatcactgtgattatgaacatt--ttaattgcagGCCCCAGGTAACAATTGCTACAGCAATCATATTTTGTCACCGTTTCTTCCTTCGTCAATCCCATGCAAAGAATGACAGAAGG
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gtaagcttgttctcttctccttcgtcttgttcttctcggaattttctttcttttcttctctcactcacactcattgacggtttgatttttttttcttgttctttcgttctttgcagCCCACAGGTGACTATTGCCACCGCAATTACATTTTGTCATCGTTTCTATCTTCGGCAATCCCATGCAAGAAACGATAGATTT
upper sequence: Vv19s0027g01670.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: EFJ27727 (Selaginella moellendorffii), 3'ss of exon 1
-------------atttcctactgttttattatttttttatgcctcaaacatgagcaaatagtttataattgtttttccagcatcactgtgattatgaacattttaat---tgcagGCCCCAGGTAACAATTGCTACAGCAATCATATTTTGTCACCGTTTCTTCCTTCGTCAATCCCATGCAAAGAATGACAGAAGG
|| | || || || || | || || | | | | | || | | | | | | || | ||| | ||||| || ||||| || ||||| || ||||| | ||||||||| ||||||| ||||| ||||||||||||| || || |||
gtaagcttgttctcttctccttcgtcttgttcttctcggatttttctttctttt-cttctctcactcagactcattgacggtttgattttttttcttgttctttcgttctttgcagCCCACAGGTGACTATTGCCACCGCAATTACATTTTGTCATCGTTTCTATCTTCGGCAATCCCATGCAAGAAACGATAGATTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atagtttataattgtttttccagcatcactgtgattatgaacattttaattgcagGCCCCAGGTAACAATTGCTACAGCAATCATATTTTGTCACCGTTTCTTCCTTCGTCAATCCCATGCAAAGAATGACAGAAGG
ttttaat putative branch site (score: 3)
attatgaacattttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atttcctactgttttattatttttttatgcctcaaacatgagcaaatagtttataattgtttttccagcatcactgtgattatgaacattttaattgcagGCCCCAGGTAACAATTGCTACAGCAATCATATTTTGTCACCGTTTCTTCCTTCGTCAATCCCATGCAAAGAATGACAGAAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - cctactg
- - - - - - - - - - - - - - gcctcaa
- - - - - - - - - - - - - - - - - - catgagc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catcact
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tatgaac