Sequence
atgc intronic sequence ATGC exonic sequence...gttaggtctctaaagattgatccttggcaacttgtaaatgttcgacgcctgggattttatgattgaaaactttaacgattgaaccaccatttgaacttagGTCTGCTTCGATGTGGAAAGAGCTGTCGGCTGCGGTGGACGAACTATCTTCGCCCAGACATTAAGCGGGGGCCCTTTACTCCGGAAGAAGAGACTGCCAT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv16s0050g00070.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os02g42870.1 (Oryza sativa), 3'ss of exon 1
--gttaggtctctaaagattgatccttggca--acttgtaaatgttcgacgcctgggattttatgattgaaaactttaacgattgaaccaccatttgaacttagGTCTGCTTCGATGTGGAAAGAGCTGTCGGCTGCGGTGGACGAACTATCTTCGCCCAGACATTAAGCGGGGGCCCTTTACTCCGGAAGAAGAGACTGCCAT
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ctctcttttcgtgcatgagaagtactcggtattattcacaggagctgagagactctagtccgttccatctgga---taacacttcgttttgcgtt-gcatgcagGGCTGAACCGGTGCGGCAAGAGCTGCCGGCTGCGGTGGACGAACTACCTCCGGCCGGACATCAAGCGCGGGCCCTTCACCGCCGAGGAGCAGAAGTCCAT
upper sequence: Vv16s0050g00070.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os04g45060.1 (Oryza sativa), 3'ss of exon 1
--------------------------------------gttaggtctctaaagattgatcct-tggcaacttgtaaatgttcgacgcctgggatttt--atgattgaaaactttaacgattgaaccaccatttgaacttagGTCTGCTTCGATGTGGAAAGAGCTGTCGGCTGCGGTGGACGAACTATCTTCGCCCAGACATTAAGCGGGGGCCCTTTACTCCGGAAGAAGAGACTGCCAT
| ||| | | || ||| | | | ||| || | |||| ||| | | | || | | | | ||| ||| || || || |||||||| |||||||||||||||||||| || || || ||||| ||||| ||||| || || ||||| || | | ||||
gtacgtacgttcgtctcttttgcgatcgatctggggccgccgcgtcgcgcgcgcgtggtccagtagtgcttccgtttcgttttttttgtgcggttttcgctgaggcgaggcgcgtgtgcgcgatcgatgggt-gcgtgcagGGCTGAACCGGTGCGGCAAGAGCTGCCGGCTGCGGTGGACGAACTACCTGCGGCCGGACATCAAGCGCGGGCCTTTCACCCCGGAGGAGCACAAGTCCAT
upper sequence: Vv16s0050g00070.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G123202_T01 (Zea mays), 3'ss of exon 2
----------------------------------------------gttaggtctctaaagattgatcc--ttggcaacttgtaaatgttcgacgcctggg-attttatgattgaaaactttaacgattgaaccac---catttgaacttagGTCTGCTTCGATGTGGAAAGAGCTGTCGGCTGCGGTGGACGAACTATCTTCGCCCAGACATTAAGCGGGGGCCCTTTACTCCGGAAGAAGAGACTGCCAT
| ||| | | ||| | ||| | | | || | || | | || | |||| | || || | | || | ||| ||| || || || |||||||| |||||||||||||| ||||| || ||||| ||||| ||||| |||| ||| || || || || | | | ||
gtacgtacgtacgtgctctgttcctcggtcgagcccagcccgggccgcctggtgctgcatgcgtgacctagttgttcgcctcgtgctcgtcatttcttgagcgactcgtggtgtaaaatgcgatgtgatgtgccgcgcgcgcatgcatgcagGGCTGAACCGGTGCGGCAAGAGCTGCCGGCTGCGGTGGACCAACTACCTGCGCCCGGACATCAAGCGCGGGCACTTCACCCCCGAGGAGCACAACTCTAT
upper sequence: Vv16s0050g00070.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G040924_T01 (Zea mays), 3'ss of exon 1
--------------------------------------------------------------------gttaggtctctaaagattgatccttggcaacttgtaaatgttcg---acgcctgggattttat-------gattgaaaactttaacg-------attgaaccaccatttg-----aactt--agGTCTGCTTCGATGTGGAAAGAGCTGTCGGCTGCGGTGGACGAACTATCTTCGCCCAGACATTAAGCGGGGGCCCTTTACTCCGGAAGAAGAGACTGCCAT
||||| ||| || | ||| || | | | || | || ||| ||| ||| | ||||| | | || || |||| ||||| | | || ||| || || || || |||||||| || ||||||||||||||||| || || || ||||| ||||| |||||||| || | || || ||| ||||
gtcggaaccatccctctcttcttgcttccatttcttcttcgcggtttccacccacacgccgtcgtcttgttag--ttctgcagctgcctccctgccggcct-caaccatacggatacggctgtgatgcttctcgctcggattgcaggcacacgcgcggtctcatctaacccccattcgcggcgcatttgcagGGCTAAACCGGTGCGGCAAGAGCTGCCGACTGCGGTGGACGAACTACCTCCGGCCGGACATCAAGCGCGGGCCCTTCACATCCGAGGAGCAGAAGTCCAT
upper sequence: Vv16s0050g00070.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA10G38090.1 (Glycine max), 3'ss of exon 1
------gttaggtctctaaagattgatccttggcaacttgtaaatgttcgacgcctgggattttatgattgaaaactttaacgattgaaccaccatttgaacttagGTCTGCTTCGATGTGGAAAGAGCTGTCGGCTGCGGTGGACGAACTATCTTCGCCCAGACATTAAGCGGGGGCCCTTTACTCCGGAAGAAGAGACTGCCAT
| | | || || || || | || || | ||| || | | ||||| || || || |||| |||||| || ||||||||||| ||||||||||| ||||||| ||||||||||| || | ||| ||||| || || |||||| |||||||| | | | ||
aaaattgacacagtccgaagga--gaaaggtgaaggcgtggttata---aagatggaggaattattaaacgaaaaaccatttaatcgatgtgtttttacaact-agGTCTCCTACGATGTGGAAAAAGCTGTCGGCTTCGGTGGATAAACTATCTTCGTCCTGGCATCAAGCGTGGCCCATTTACTAGTGAAGAAGAAAGTACAAT
upper sequence: Vv16s0050g00070.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA20G29730.1 (Glycine max), 3'ss of exon 1
-gttaggtctctaaagattgatccttggcaacttgtaaatgttcgacgcctgggattttatgattgaaaac--tttaacgattgaaccaccatttgaacttagGTCTGCTTCGATGTGGAAAGAGCTGTCGGCTGCGGTGGACGAACTATCTTCGCCCAGACATTAAGCGGGGGCCCTTTACTCCGGAAGAAGAGACTGCCAT
| | | | ||| || || | | || | | || ||| | | |||| ||||| | | | | | ||||||| || |||||||||| || |||||||| ||||||| |||||||||||||||| ||| ||||| || || |||||| |||||||| | | | ||
gctccactatatgaagga-gaaaggtgaaagc--gtggttataaagatggaggaattattcaacgaaaaatcatttaatcaatatatttttacaatgaactagGTCTCCTAAGATGTGGAAAAAGTTGTCGGCTTCGGTGGATAAACTATCTTCGCCCAGGCATCAAGCGTGGCCCATTTACTAGTGAAGAAGAAAGTACAAT
upper sequence: Vv16s0050g00070.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: PP1S326_37V6.1 (Physcomitrella patens), 3'ss of exon 1
gttaggtctctaaag-attgatccttggcaacttgtaaatgttcgacgcctgggattttatgattgaaaactt-taacgattgaaccaccatttgaacttagGTCTGCTTCGATGTGGAAAGAGCTGTCGGCTGCGGTGGACGAACTATCTTCGCCCAGACATTAAGCGGGGGCCCTTTACTCCGGAAGAAGAGACTGCCAT
| || | | | || | | | | | | | |||| || ||| || || | | | || || | ||| | ||| || | || || ||||||||| |||||||||||||||||||||| | || ||||| ||||| || | || ||| || || || ||
aatgggcagtgagatcaatggaattgagtcatgtttcaggg--cgacaaagtagagtttctgtctgcagtcccattctgagtgcgcattttttttctttcagGGCTTGCGAGGTGCGGCAAGAGCTGTAGGCTGCGGTGGACGAACTATCTGAGACCTGACATCAAGCGAGGACGATTCTCTCACGAGGAGGACCAGATGAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cgcctgggattttatgattgaaaactttaacgattgaaccaccatttgaacttagGTCTGCTTCGATGTGGAAAGAGCTGTCGGCTGCGGTGGACGAACTATCTTCGCCCAGACATTAAGCGGGGGCCCTTTACTCCGGAAGAAGAGACTGCCAT
ctttaac putative branch site (score: 3)
attttatgattgaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttaggtctctaaagattgatccttggcaacttgtaaatgttcgacgcctgggattttatgattgaaaactttaacgattgaaccaccatttgaacttagGTCTGCTTCGATGTGGAAAGAGCTGTCGGCTGCGGTGGACGAACTATCTTCGCCCAGACATTAAGCGGGGGCCCTTTACTCCGGAAGAAGAGACTGCCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - tccttgg
- - - - - - - - - - - - - - - - - - - - - cgacgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttgaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - accacca