Sequence
atgc intronic sequence ATGC exonic sequence...tcacatgaaaacacatccaaatttccttaagcaatggaattgctgcctacatattttggtaaaaccatgttgttgataatgttttcctatgaaactgcagATGATGTTATATGGGGCAATATTTGGTTGCTTATCACCCATTCTCTCAATTTCAGCATTTTTGAGCTATAAGTCACCATTTTTATCTCCAAAAGATGAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv12s0035g00800.t01 (Vitis vinifera), 3'ss of exon 23
lower sequence: LOC_Os04g35260.1 (Oryza sativa), 3'ss of exon 24
-tcacatgaaaacacatccaaatttccttaagcaatggaattgctgcc-tacatattttggtaaaaccatgttgttgataatgttttcctatgaaactgcagATGATGTTATATGGGGCAATATTTGGTTGCTTATCACCCATTCTCTCAATTTCAGCATTTTTGAGCTATAAGTCACCATTTTTATCTCCAAAAGATGAG
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atgacagtaattgttatgtttgttccatcgatttgtggagcatttgtagtactttacctatttaa--tgttttgctttgatttgtcttctgtgcgactgcagATGATGCTCTATGGTGCTATCTTTGGCTGCTTATCTCCCATTCTTTCTGTTGCTGCTTTTCTGAGTTATAAATCCCCATTCATCTCTCCAAAAGATGAG
upper sequence: Vv12s0035g00800.t01 (Vitis vinifera), 3'ss of exon 23
lower sequence: GRMZM2G013283_T01 (Zea mays), 3'ss of exon 24
-------tcacatgaaaacacatccaaatttcc-ttaagcaatggaattgctgcctacatattttggtaaaaccatgttgttgataatgttttcctatgaaactgcagATGATGTTATATGGGGCAATATTTGGTTGCTTATCACCCATTCTCTCAATTTCAGCATTTTTGAGCTATAAGTCACCATTTTTATCTCCAAAAGATGAG
|||| | | ||||| || |||||| | | |||| | | | || || | || ||||| |||| |||||||||||| | ||||| || || |||||||| |||||||| ||||| || || | || || |||| ||||| || |||||| | |||||||||||||||
atttctgcttcatgcattttgttgtgaatttatatttctttatggaacttttct-------tttttgcacactgatattccgattcat-ttttcatatgcggctgcagATGATGCTTTATGGTGCTATCTTTGGTTGTTTATCACCAATTCTGTCCGTTGCTGCTTTCCTGAGTTATAAATCTCCATTTCTCTCTCCAAAAGATGAG
upper sequence: Vv12s0035g00800.t01 (Vitis vinifera), 3'ss of exon 23
lower sequence: AT1G58060.1 (Arabidopsis thaliana), 3'ss of exon 25
tcacatgaaaacacatccaaatttc--cttaagcaatggaattgctgcctacatattttg--gtaaaaccatgtt----gttgataatgttttcctatgaaactgcagATGATGTTATATGGGGCAATATTTGGTTGCTTATCACCCATTCTCTCAATTTCAGCATTTTTGAGCTATAAGTCACCATTTTTATCTCCAAAAGATGAG
| | | |||| | | || ||| | | | | | | || || | | | ||| | | | || |||||||| ||||||| || | ||||||||||||||||||||| |||||||| || |||| || |||||||| || || || ||| ||| ||| |||||||||
--------attgctgcctaggtttcaacatggttgttgatgttgataaccagagagtgcatcatagaattctttccaccatcatgaatatatgtttgataatttgcagATGCTGTTATACGGTGGAATATTTGGTTGCTTATCACCTATTCTCTCGATCGCAGCTTTCTTGAGCTACAAATCGCCGTTTATATATCCCAAAGATGAG
upper sequence: Vv12s0035g00800.t01 (Vitis vinifera), 3'ss of exon 23
lower sequence: AT1G58050.1 (Arabidopsis thaliana), 3'ss of exon 25
tcacatgaaaacacatccaaatttccttaagcaatggaattgctg--cctacatattttggtaaaac---catgttgttgataatgtttt-cctatgaaac--tgcagATGATGTTATATGGGGCAATATTTGGTTGCTTATCACCCATTCTCTCAATTTCAGCATTTTTGAGCT---ATAAGTCACCATTTTTATCTCCAAAAGATGAG
||| ||| || || |||| || | | | | | | |||| | ||||| | | ||| | ||| |||||||| |||||||||| | || ||||||||||||||||| |||||||| ||| | || || ||||||| || || || ||| ||| | | |||||||
--------------------gtttgcttcagtaacatcattgttgtactaataaaggccgctcaaacatatgttttgttatcatcactacaccttttaaataatgcagATGCTGTTATATGGTGGCATTTTTGGTTGCTTATCACCTATTCTCTCGATTGCTGCTTTCTTGAGCTGCTGCAAATCGCCGTTTGTATATGCCAAAGATG-- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cctacatattttggtaaaaccatgttgttgataatgttttcctatgaaactgcagATGATGTTATATGGGGCAATATTTGGTTGCTTATCACCCATTCTCTCAATTTCAGCATTTTTGAGCTATAAGTCACCATTTTTATCTCCAAAAGATGAG
tgttgat putative branch site (score: 4)
atattttggtaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcacatgaaaacacatccaaatttccttaagcaatggaattgctgcctacatattttggtaaaaccatgttgttgataatgttttcctatgaaactgcagATGATGTTATATGGGGCAATATTTGGTTGCTTATCACCCATTCTCTCAATTTCAGCATTTTTGAGCTATAAGTCACCATTTTTATCTCCAAAAGATGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
tcacatg
- - - - - - acatcca
- - - - - - - - - - - - - - - - aatggaa
- - - - - - - - - - - - - - - - - - - - - - gcctaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaccat