Sequence
atgc intronic sequence ATGC exonic sequence...ggatatctggagaattttaaaagctacaatgacagaatctggaccctgtataaaatttatatttgatcatgaattttgttgtttgctttattggaaacagGTCCAGGTGGGTGGTTCTCCAGTTTACAAAATTGATAGAAAACTGGGGAAAGGAGGCTTTGGACAAGTTTATGTTGGGCGACGCATTGGTGGAAATTCAA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv04s0008g00160.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: PP1S131_16V6.1 (Physcomitrella patens), 3'ss of exon 1
ggatatctggagaattttaaaagctacaatgacagaatctggaccctgta----taaaatttatatttgatcatgaattttgttgtttgctttattggaaa----cagGTCCAGGTGGGTGGTTCTCCAGTTTACAAAATTGATAGAAAACTGGGGAAAGGAGGCTTTGGACAAGTTTATGTTGGGCGACGCATTGGTGGAAATTCAA
| ||| || | | | ||| | | | | | ||||||||| ||| | || | | | || | || ||||| || || || || || ||||| ||||| || || || ||||| || |||||||||||||||||||| |||||||| || || | | || ||
--------atataatgttgcactccctctctgtatcttctttatttttttatttttcattttatattttatcctatatcattgagcctaacttgtgctcaatgcgcagGTTCAAGTTGGCGGCTCACCAGTGTACAAGATAGAGAGGAAACTCGGAAAAGGAGGCTTTGGACAAGTCTATGTTGGTCGTCGGCTAAGCGGTGGGACAG
upper sequence: Vv04s0008g00160.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: PP1S66_174V6.1 (Physcomitrella patens), 3'ss of exon 1
ggatatctggagaattttaaaagcta-caatgacagaatctgg-accctgt-ataaaatttatatttgatcatgaattttgttgtttgctttattggaa-acagGTCCAGGTGGGTGGTTCTCCAGTTTACAAAATTGATAGAAAACTGGGGAAAGGAGGCTTTGGACAAGTTTATGTTGGGCGACGCATTGGTGGAAATTCAA
| | | || ||||| | |||| || | || | || | | ||| ||| ||| | | | ||| || | ||||| || || ||||| |||||||| ||||| ||||| || ||||| || || ||||||||||| ||||| |||||||| || || | |||| ||
----gtgtcatggatggacgcagctaactatgatggagtgcggcatgtcgtgacattattactatgtgagttgttactgacctccttgtattctgaatgcgcagGTTCAAGTTGGTGGCTCTCCAGTCTACAAGATTGAGAGGAAACTTGGAAAGGGAGGCTTTGGTCAAGTATATGTTGGTCGTCGTCTCAGTGGTGGGGCAG
upper sequence: Vv04s0008g00160.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: EFJ19085 (Selaginella moellendorffii), 3'ss of exon 1
ggatatctggagaattttaaaagctacaatgacagaatctggaccctgtataaaatttatatttgatcatgaattttgttgtttgctttattggaaacagGTCCAGGTGGGTGGTTCTCCAGTTTACAAAATTGATAGAAAACTGGGGAAAGGAGGCTTTGGACAAGTTTATGTTGGGCGACGCATTGG---TGGAAATTCAA
| || | | || || | || | | || | |||| |||| ||| || ||| | || || ||||||||||| || || | | ||||| || |||||||||||||||||||| |||||||| || || || | || ||| ||
-------------------------------gtatgattt---ttttccattggatgtggatgtaactttgcaatttg--gtttcttttgttt---ccagATACAAGTTGGTGGTTCTCCGGTCTATAGGACGGATAGGAAGCTGGGGAAAGGAGGCTTTGGTCAAGTTTACGTGGGTCGGAAGTTGGGGCCTGGTGATC---
upper sequence: Vv04s0008g00160.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: EFJ13521 (Selaginella moellendorffii), 3'ss of exon 1
ggatatctggagaattttaaaagctacaatgacagaatctggaccctgtataaaatttatatttgatcatgaattttgttgtttgctttattggaaacagGTCCAGGTGGGTGGTTCTCCAGTTTACAAAATTGATAGAAAACTGGGGAAAGGAGGCTTTGGACAAGTTTATGTTGGGCGACGCATTGG---TGGAAATTCAA
| || | | || || | || | | || | |||| |||| || || ||| | || || ||||||||||| || || | | ||||| || |||||||||||||||||||| |||||||| || || || | || ||| ||
-------------------------------gtatgattt---ttttccatcggatgtggatgtaactttgcaatttg--gtttctcttgttc----cagATACAAGTTGGTGGTTCTCCGGTCTATAGGACGGATAGGAAGCTGGGGAAAGGAGGCTTTGGTCAAGTTTACGTGGGTCGGAAGTTGGGGCCTGGTGATC--- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctgtataaaatttatatttgatcatgaattttgttgtttgctttattggaaacagGTCCAGGTGGGTGGTTCTCCAGTTTACAAAATTGATAGAAAACTGGGGAAAGGAGGCTTTGGACAAGTTTATGTTGGGCGACGCATTGGTGGAAATTCAA
atttgat putative branch site (score: 5)
ctttatt putative PPT
taaaatttatatttga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ggatatctggagaattttaaaagctacaatgacagaatctggaccctgtataaaatttatatttgatcatgaattttgttgtttgctttattggaaacagGTCCAGGTGGGTGGTTCTCCAGTTTACAAAATTGATAGAAAACTGGGGAAAGGAGGCTTTGGACAAGTTTATGTTGGGCGACGCATTGGTGGAAATTCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - -taaaagc
- - - - - - - - - - - - - - - - - - - - - accctgt
- - - - - - - - - - - - - - - - - - - - - - - - -ataaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gatcatg