Sequence
atgc intronic sequence ATGC exonic sequence...gataaagtgtaatcagttttatttgaaattccaacacttctaatgaattttttaattgtttttcagatgatttgatgaatggtttatctaaatgttgcagATTTTGAGGAAGCTGAAACATGAAAATATCATTGAAATGCTCGACTCCTTTGAGACCCCTCAAGAGTTCTGCGTTGTCACAGAATTTGCACAA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv16s0039g02400.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G062524_T02 (Zea mays), 3'ss of exon 2
gataaagtgtaat-cagttttatttgaaattccaacacttctaatgaatt-ttttaattgtttt-tcagatgatttga-tgaatggt-ttatcta-aatgttgcagATTTTGAGGAAGCTGAAACATGAAAATATCATTGAAATGCTCGACTCCTTTGAGACCCCTCAAGAGTTCTGCGTTGTCACAGAATTTGCACAA
| || | ||| | ||| | | || | || ||| | || | | | | | |||| | | || | | || | ||| || |||| | ||||| || |||||||| || || ||||||||| |||| ||||||| |||||||| ||||| || ||||||||||| ||||| ||
------ctacgattcggttgtgcttgtcaaattagcattattaggcaatggcgctccttatctcattataccatttcacttcttgatgtcatacacaattctgtagATCCTAAGGAAACTCAAACATGAGAACATAATTGAAATGATCGATGCCTTTGAAACCCCTCAGGAGTTTTGTGTTGTCACAGAGTTTGCTCAG
upper sequence: Vv16s0039g02400.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA20G16860.1 (Glycine max), 3'ss of exon 2
gataaagtgtaatcagttttatttgaaattccaacactt--ctaatgaattttttaattgtttttcagatgatt--tgatgaatggtttatctaaatgttgcagATTTTGAGGAAGCTGAAACATGAAAATATCATTGAAATGCTCGACTCCTTTGAGACCCCTCAAGAGTTCTGCGTTGTCACAGAATTTGCACAA
| | | || | | | ||| || || | || |||| ||| || |||| | ||| | ||| || | ||||| |||||||| || || ||| |||| |||| |||||| ||| ||||||| || |||||||| | ||| ||||| || || ||||| |||||||||||||||
----atttattattgttgctgctaattattataattattaatttattaattacttataagtgtttctgctgactagtgacatttgaaattcataaattttgcagATCTTAAGAAAGTTGAAGCATGGAAATATTATTCAAATGCTTGATTCCTTTGAAAGCCCGCAAGAATTTTGTGTTGTTACAGAATTTGCACAA
upper sequence: Vv16s0039g02400.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA10G22860.1 (Glycine max), 3'ss of exon 2
gataaagtgtaatcagttttatttgaaattccaacacttctaatgaattttttaattgtttttcagatgatt--tgatgaatggtttatctaaatgttgcagATTTTGAGGAAGCTGAAACATGAAAATATCATTGAAATGCTCGACTCCTTTGAGACCCCTCAAGAGTTCTGCGTTGTCACAGAATTTGCACAA
| || | | | | || || || | | | | || |||| ||| || |||| | ||| | ||| || | ||||| |||||||| || | ||| | || |||| |||||| ||| |||||||||| |||||||| | ||| ||||| || || ||||| |||||||||||||||
-tttaattattgttgttgctaattattataatta-attatttattaattacttataagtgtttctgctgactggtgacatgtgacattcataaattttgcagATCTTACGAAAGTTAAAGCATGGAAATATTATTCAAATGCTCGATTCCTTTGAAAGCCCGCAAGAATTTTGTGTTGTTACAGAATTTGCACAA
upper sequence: Vv16s0039g02400.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT1G50240.2 (Arabidopsis thaliana), 3'ss of exon 2
gataaagtgtaatcagttttatttgaaatt-ccaacacttctaatgaattttttaattgtttttcagatgatttgatgaatggtttatctaa-atgttgcagATTTTGAGGAAGCTGAAACATGAAAATATCATTGAAATGCTCGACTCCTTTGAGACCCCTCAAGAGTTCTGCGTTGTCACAGAATTTGCACAA
| || || ||| ||| | || ||| || | |||| ||| |||| | | |||||| || | | ||| ||| ||||| ||| ||||||| || ||||| ||||||||||||||||||||||||||||| | | | | ||||||||| || ||||| || ||||| |||
gttagcaagtttcagtccttaattgcacttaccatcaactttaat------cccaatcaattttatggt-atttgaccaacattatttcttttatgcctcagATATTGCGGAAGCTCAAGCATGAGAATATCATTGAAATGCTCGACTCCTTTGAAAACGCACGAGAGTTCTGTGTCGTCACTGAGTTTGCCCAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aattttttaattgtttttcagatgatttgatgaatggtttatctaaatgttgcagATTTTGAGGAAGCTGAAACATGAAAATATCATTGAAATGCTCGACTCCTTTGAGACCCCTCAAGAGTTCTGCGTTGTCACAGAATTTGCACAA
atctaaa putative branch site (score: 3)
tttaattgtttttca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gataaagtgtaatcagttttatttgaaattccaacacttctaatgaattttttaattgtttttcagatgatttgatgaatggtttatctaaatgttgcagATTTTGAGGAAGCTGAAACATGAAAATATCATTGAAATGCTCGACTCCTTTGAGACCCCTCAAGAGTTCTGCGTTGTCACAGAATTTGCACAA
gataaag
- - - - - - - - - - - - - - - ccaacac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgaatgg