Sequence
atgc intronic sequence ATGC exonic sequencegtaactggtaccctcaagctgtttgtgatggatggtttgtattgcattaatgatgtgatacacaaatttttgcagCTGAACTTGTTGAAAGAGTTGTTCTTCTTGGAGCACCCATTTCGTTCAGAGATGAGAACTGGGAAGTTGCTAGAAAA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv04s0023g02940.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA01G37420.1 (Glycine max), 3'ss of exon 11
------------------------gtaactggtaccctcaagctgtttgtgatggatggtttgtattgcattaatgatgtgatacacaaatt--tttgcagCTGAACTTGTTGAAAGAGTTGTTCTTCTTGGAGCACCCATTTCGTTCAGAGATGAGAACTGGGAAGTTGCTAGAAAA
| || || | | | | | || | || ||| | || ||| | | || || ||||||||||| || || ||||||||||||||||||||||||||| | ||| || ||||| ||||||| |||||||||
ggttattttacatattatatcatttctatggggactcgtgcgtt-tatctgttaaataagatgttcccttattctggggtgctgcttctgtttattggcagCTGAACTGGTAGAGAGAGTTGTTCTTCTTGGAGCACCCATTGCAATCAAGGACGAGAATTGGGAAGCTGCTAGAAAG
upper sequence: Vv04s0023g02940.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA02G05680.1 (Glycine max), 3'ss of exon 11
-------------------gtaactggtaccctcaagct-gtttgt--gatggatggtt--tgtattgcattaatgatgtgatacacaaatttttg-cagCTGAACTTGTTGAAAGAGTTGTTCTTCTTGGAGCACCCATTTCGTTCAGAGATGAGAACTGGGAAGTTGCTAGAAAA
| | | ||| | | | || ||| ||| |||| | || | | || | ||| ||| ||||||||||||| |||| |||||| ||||||||||||||||| | ||| |||||||||||||||| |||||||
gatggatgcatataatttaatgtcccttcttttcatgtttatccgttgaatgagacgttaccatattacttttaatgtctgccctgcttattattgacagCTGAACTTGTAGAAAAAGTTGTACTTCTTGGAGCACCCATCCCAATCATGGATGAGAACTGGGAAGCAACTAGAAAG
upper sequence: Vv04s0023g02940.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA11G07870.1 (Glycine max), 3'ss of exon 10
----------------------gtaactggtaccctcaagctgtttgtgatggatggtttgtattgcattaat---gatgtgatacacaaatt--tttgcagCTGAACTTGTTGAAAGAGTTGTTCTTCTTGGAGCACCCATTTCGTTCAGAGATGAGAACTGGGAAGTTGCTAGAAAA
| | | | | | | ||||| | |||| | | | ||| || || | | | || || ||||||||||| || || |||||||||||||||||| ||||||| | ||| |||||||| ||||||| |||||||||
agatattatatgatttctgtgggggaatcatgcgtttat-ctgttaaata-agatgttccctttcttattgattccgaggcactgcttctgtttattggcagCTGAACTGGTCGAGAGAGTTGTTCTTCTTGGATTACCCATTGCAATCAAGGATGAGAATTGGGAAGCTGCTAGAAAG
upper sequence: Vv04s0023g02940.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA16G24310.1 (Glycine max), 3'ss of exon 11
-----------------------gtaactg-gtaccctcaagctgtttgt--gatggatggtttgtattgcattaatgatgtgatacacaaatttttgcagCTGAACTTGTTGAAAGAGTTGTTCTTCTTGGAGCACCCATTTCGTTCAGAGATGAGAACTGGGAAGTTGCTAGAAAA
|| || ||| || ||||| | | || || | || |||| | || | | || |||||||||| || |||| |||||| ||||||||||||||||| | ||| |||||||||||||||| ||||||||
gtgatggatgcttataatttaatgtccttgcatactctttccatgtttatccgttgagtgaggt-taccatattactttaatgtctgcttattattgacagCTGAACTAGTAGAAAAAGTTGTGCTTCTTGGAGCACCCATCCCAATCAAGGATGAGAACTGGGAAGCAGCTAGAAAG
upper sequence: Vv04s0023g02940.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA17G17160.1 (Glycine max), 3'ss of exon 9
-----------------gtaactg-gtaccctcaagctgtttgt--gatggat--ggtt--tgtattgcattaatgatgtgatacacaaatttttg-cagCTGAACTTGTTGAAAGAGTTGTTCTTCTTGGAGCACCCATTTCGTTCAGAGATGAGAACTGGGAAGTTGCTAGAAAA
|| || ||| || ||||| | | || | |||| |||| | || | | || | ||| ||| |||||||||| || |||| |||||| ||||||||||||||||| | ||| ||||||||| |||||| ||||||||
ggatgcattaatttaatgtccttgcatactctttccatgtttatccgttgagtgaggttaccatattacttttaatgtctgccctgcttattattgacagCTGAACTAGTAGAAAAAGTTGTGCTTCTTGGAGCACCCATCCCAATCAAGGATGAGAACGGGGAAGCAGCTAGAAAG
upper sequence: Vv04s0023g02940.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: AT4G36210.1 (Arabidopsis thaliana), 3'ss of exon 10
gtaactggtaccct-caagct----gtttgtgatggatggtttgtattgcattaatgatgtgatacacaaatttttg-cagCTGAACTTGTTGAAAGAGTTGTTCTTCTTGGAGCACCCATTTCGTTCAGAGATGAGAACTGGGAAGTTGCTAGAAAA
|||| | | | |||| | | ||| | | | | | ||| || | ||| | |||| |||||||||||| || ||||||||||||||||||||||||||||| ||| ||| |||||| || | || ||
gtaatttccaatgtgcaagatagaagattgctttaaaagatcaaatctttcttacggagactcttaacatgtctttggtagCTGAACTTGTGGAGAGAGTTGTTCTTCTTGGAGCACCCATTTCAATCAATAGTGAAAACTGGCGAGACGTAAGGAAG
upper sequence: Vv04s0023g02940.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: AT2G18100.1 (Arabidopsis thaliana), 3'ss of exon 11
gtaactggt-accctcaagctgtttgtgatggatggtttgtattgcattaatga-tgtgatacacaaatttttgcagCTGAACTTGTTGAAAGAGTTGTTCTTCTTGGAGCACCCATTTCGTTCAGAGATGAGAACTGGGAAGTTGCTAGAAAA
||| | || | | | | | || | | || | | ||| || | | | ||| | | ||||||| |||| |||||||||||||||||||||||||| ||||| ||| ||||||| ||| || | |||||
gtatttctccactcaatatttatctttgctttagaattgacaattgattcttgtctttaacacatttttcacggtagCTGAAATTGTGGAAAGAGTTGTTCTTCTTGGAGCACCAATTTCAATCAAGAATGAGAATTGGCGAGACGTAAGAAAGMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|110360866|gb|EC924300.1|EC924300EST: ACGAGTGATTTTCAAGTGTCTGCAGTATTTGGCTGAAACTGAACAAAATG CTGAACTTGTTGAAAGAGTTGTTCTTCTTGGAGCACCCATTTCGTTCAGAG
genomic: ACGAGTGATTTTCAAGTGTCTGCAGTATTTGGCTGAAACTGAACAAAATGgtaactggta ... atttttgcagCTGAACTTGTTGAAAGAGTTGTTCTTCTTGGAGCACCCATTTCGTTCAGAG
EST:
gi|33401930|gb|CF207557.1|CF207557EST: ACGAGTGATTTTCAAGTGTCTGCAGTATTTGGCTGAAGCTGAACAAAATG CTGAACTTGTTGAAAGAGTTGTTCTTCTTGGAGCACCCATTTCGTTCAGAG
genomic: ACGAGTGATTTTCAAGTGTCTGCAGTATTTGGCTGAAACTGAACAAAATGgtaactggta ... atttttgcagCTGAACTTGTTGAAAGAGTTGTTCTTCTTGGAGCACCCATTTCGTTCAGAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtttgtgatggatggtttgtattgcattaatgatgtgatacacaaatttttgcagCTGAACTTGTTGAAAGAGTTGTTCTTCTTGGAGCACCCATTTCGTTCAGAGATGAGAACTGGGAAGTTGCTAGAAAA
cattaat putative branch site (score: 3)
tttttgc putative PPT
atacacaaattttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaactggtaccctcaagctgtttgtgatggatggtttgtattgcattaatgatgtgatacacaaatttttgcagCTGAACTTGTTGAAAGAGTTGTTCTTCTTGGAGCACCCATTTCGTTCAGAGATGAGAACTGGGAAGTTGCTAGAAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG