Sequence
atgc intronic sequence ATGC exonic sequence...gcccatgcttgcaagttcatcaaagttctaatcctaattgaactgtgactgatttgagttcattggggatggcaataataaaatgtttctaatcatgcagGCAATAGAAGTTGTTGATCCAGACCAAAAGATTAAAATGGTTGAGGAGCTTGATGGTCATATCATGCGATGTGTGCGTGATCAGAATGGAAACCATGTCA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv06s0004g05100.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os01g62650.1 (Oryza sativa), 3'ss of exon 5
gcccatgcttgcaagttcatcaaagttctaatcctaattgaactgtgactgatttgagttcattggggatggcaataataaa-atgtttctaatcatgcagGCAATAGAAGTTGTTGATCCAGACCAAAAGATTAAAATGGTTGAGGAGCTTGATGGTCATATCATGCGATGTGTGCGTGATCAGAATGGAAACCATGTCA
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--------------gtactgcatggct-tggctctgtttcttttttg--tgaaaaaaaatattcttatctttcaatgatatttatattcacattactgaagGCAATAGAAGTGGTTGACCTGGACCAGAAGACAAAAATGGTTACTGAGCTTGATGGCCATATCATGAGATGCGTGCGTGATCAAAATGGAAACCATGTTA
upper sequence: Vv06s0004g05100.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA15G04060.2 (Glycine max), 3'ss of exon 6
--------gcccatgcttgcaagttcatcaaagttctaatcctaattgaactgtgactgatttgagttcattggggatggcaataataaaatgtttctaatcatg-----cagGCAATAGAAGTTGTTGATCCAGACCAAAAGATTAAAATGGTTGAGGAGCTTGATGGTCATATCATGCGATGTGTGCGTGATCAGAATGGAAACCATGTCA
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gtattcacagctatgggtgctagtatttgacatttctatgtatggct---ctgtatcca--taatgttc--tgaagatgccatccttctatatttttttattgtgctcttcagGCCATAGAAGTTGTTGATCTGGACCAGAAGATAAAGATGGTTCAAGAACTTGATGGAAATATCATGCGTTGTGTGCGAGATCAGAATGGCAATCATGTAA
upper sequence: Vv06s0004g05100.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA12G06450.3 (Glycine max), 3'ss of exon 5
---------------------gcccatgcttgcaagttcatcaaagttctaatcctaattgaactgtgactgatttgagttcattggggatggcaataataaaatgtttctaatcatgcagGCAATAGAAGTTGTTGATCCAGACCAAAAGATTAAAATGGTTGAGGAGCTTGATGGTCATATCATGCGATGTGTGCGTGATCAGAATGGAAACCATGTCA
| | || | | || | | | || | | ||| || || ||||| | | | | | | | | |||| || ||||||||||||| || || ||||| | |||||| | |||||||||||| || | ||||| ||||| |||||||||||||| || |||||||
gtatggacaatataaggtgctggtggcattagctgatatgtataatatttgactctg-taattttctgaatgtctta---tcatttttctttttttctttccattatgtattcctctttagGCCATCGAAGTTGTTGATCTGGATCAGAAGATAGAGATGGTTCAAGAGCTTGATGGTAATGTTATGCGCTGTGTACGTGATCAGAATGGTAATCATGTCA
upper sequence: Vv06s0004g05100.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA12G06430.1 (Glycine max), 3'ss of exon 4
----------------------------gcccatgcttgcaagttcatcaaagttctaatcctaattgaactgtgactgatttgagttcattggggatggcaataataaaatgtttctaatcatgcagGCAATAGAAGTTGTTGATCCAGACCAAAAGATTAAAATGGTTGAGGAGCTTGATGGTCATATCATGCGATGTGTGCGTGATCAGAATGGAAACCATGTCA
| || | | | ||| | | | | ||| || || | || | ||| | | | || | | ||| || ||||||||||||| || || ||||| | |||||| | |||||||||||| || | ||||| ||||| |||||||||||||| || |||||||
gtatgggcaatataaggtggctggtgggtgtggcattagctgatatgtatatgtttgaccctctgtaattttctgaatgtcttatcatttttttttgttctttcaattatgtatccctcttta----gGCCATTGAAGTTGTTGATCTGGATCAGAAGATAGAGATGGTTCAAGAGCTTGATGGTAATGTTATGCGCTGTGTACGTGATCAGAATGGTAATCATGTCA
upper sequence: Vv06s0004g05100.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA11G14550.1 (Glycine max), 3'ss of exon 7
---------gcccatgcttgca--agttcatcaaagttctaatcctaattgaactgtgactgatttgagttcattggggatggcaataataaaatgtttctaatcatgcagGCAATAGAAGTTGTTGATCCAGACCAAAAGATTAAAATGGTTGAGGAGCTTGATGGTCATATCATGCGATGTGTGCGTGATCAGAATGGAAACCATGTCA
||| ||||| |||| || | || | | | | | ||||||| ||||| | | || | | | | | |||| || ||||||||||||| || || ||||| | |||||| | |||||||||||| || ||||||| ||||| || ||||||||||| || |||||||
gtatggacaatatatggttgcattagttgat--atgtatatgtttgactctataattttctgatttcttatcatttttcttttgttctttgaattatgtatcccactttagGCCATTGAAGTTGTTGATCTGGATCAGAAGATAGAGATGGTTCAAGAGCTTGATGGTAATGTCATGCGCTGTGTACGCGATCAGAATGGTAATCATGTCA
upper sequence: Vv06s0004g05100.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA11G14500.1 (Glycine max), 3'ss of exon 6
---------gcccatgcttgcaagttcatcaaagttctaatcctaattgaactgtgactgatttgagt------tcattggggatggcaataataaaatgtttctaatcatgcagGCAATAGAAGTTGTTGATCCAGACCAAAAGATTAAAATGGTTGAGGAGCTTGATGGTCATATCATGCGATGTGTGCGTGATCAGAATGGAAACCATGTCA
|| ||||| || | | | || | | |||| | | | ||| | ||||| | | || | | | | | | |||| || ||||||||||||| || || ||||| | |||||| | |||||||||||| | ||||||| ||||| |||||||||||||| || || ||||
gtattgagaatatttggttgca--ttagttgatatgtatatgtttgtccctctgtaattt-tctgaatgccttatcatttttcttttgttctttcaattatatatctccctttagGCCATCGAAGTTGTTGATCTGGATCAGAAGATAGAGATGGTTCAAGAGCTTGATGGTAACGTCATGCGCTGTGTACGTGATCAGAATGGTAATCACGTCA
upper sequence: Vv06s0004g05100.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA11G14530.1 (Glycine max), 3'ss of exon 5
---------gcccatgcttgca--agttcat---caaagttctaatcctaattgaactgtgactgatttgagttcattggggatggcaataataaaatgtttctaatcatgcagGCAATAGAAGTTGTTGATCCAGACCAAAAGATTAAAATGGTTGAGGAGCTTGATGGTCATATCATGCGATGTGTGCGTGATCAGAATGGAAACCATGTCA
||| ||||| |||| || | | | | | || || | | | | || | | ||| | | | | || | | | | |||| || ||||||||||||| || || ||||| | |||||| | |||||||||||| | ||||||| ||||| || ||||||||||| || |||||||
gtatggacaatatatggttgcattagttgatatgtatatgtttgactctctctggaattttcttaatgtcttataattttcttttgttctt-tcaattatatacccctctttagGCCATCGAAGTTGTTGATCTGGATCAGAAGATAGAGATGGTTCAAGAGCTTGATGGTAACGTCATGCGCTGTGTACGCGATCAGAATGGTAATCATGTCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgactgatttgagttcattggggatggcaataataaaatgtttctaatcatgcagGCAATAGAAGTTGTTGATCCAGACCAAAAGATTAAAATGGTTGAGGAGCTTGATGGTCATATCATGCGATGTGTGCGTGATCAGAATGGAAACCATGTCA
ttctaat putative branch site (score: 2)
aataataaaatgtttc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcccatgcttgcaagttcatcaaagttctaatcctaattgaactgtgactgatttgagttcattggggatggcaataataaaatgtttctaatcatgcagGCAATAGAAGTTGTTGATCCAGACCAAAAGATTAAAATGGTTGAGGAGCTTGATGGTCATATCATGCGATGTGTGCGTGATCAGAATGGAAACCATGTCA
- ccatgct
- - - - - - - - tcatcaa
- - - - - - - - - - - - - - - - - -aattgaa
- - - - - - - - - - - - - - - - - - - - - - -tgactga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gggatgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aataaaa