Sequence
atgc intronic sequence ATGC exonic sequence...gagaataattttgcaacttcagtgttctgctgtagttcattaccaattacacttgcttcagtttgcattgactgtttgtctatccatcttgccgttacagATTGCGGATTTCTGGAAGGAGGCTTTGATATTGAGTTCATTACATCATCCAAATGTCGTTTCCTTTTATGGTATAGTTCGTGATGGCCCTGGTGGCTCTT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv11s0052g01480.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os02g54510.3 (Oryza sativa), 3'ss of exon 4
-------------------------------------gagaataattttgcaacttcagtgttc--tgctgtagttcattaccaat----------------tacacttgcttcagtttgcatt--------gactgtttgtctatccatct---tgccgttacagATTGCGGATTTCTGGAAGGAGGCTTTGATATTGAGTTCATTACATCATCCAAATGTCGTTTCCTTTTATGGTATAGTTCGTGATGGCCCTGGTGGCTCTT
|| | |||| | ||| | ||| || | || | | || | ||||||| || | | || | || | || | || || |||||||| ||||||||||| || ||| ||| | |||||| | |||||||||||||| ||||| ||||||||| |||||||||| || |||| ||| |
gtatgcttgattgacttgttaacaccttagaacttttaggattgatttcatagctttttttttccttgttaaagatttctgttaaaaccctctggatagtgattttcttgcttttgtgtattctatggagaagatctctagttcagatatatatgtggttttgcagATTGCTGATTTCTGGAAAGAAGCTCAGATTCTAAGTTCACTTCATCATCCAAATGTGGTTTCATTTTATGGTGTAGTTCGTGACGGTCCTGATGGAAGCT
upper sequence: Vv11s0052g01480.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G052658_T01 (Zea mays), 3'ss of exon 3
gagaataat-tttgcaacttcagtgttctgctgtagttcattaccaatt---acacttgcttcagtttgcattgactgtttgtct-atccatcttgccgttacagATTGCGGATTTCTGGAAGGAGGCTTTGATATTGAGTTCATTACATCATCCAAATGTCGTTTCCTTTTATGGTATAGTTCGTGATGGCCCTGGTGGCTCTT
||| || ||| | || | | |||| || | |||| ||| | ||| ||| | ||| | | || || |||| || |||||||||||||||||||| || ||| |||| | || ||| | |||||||||||||| ||||| ||||||||| ||||||||||||| || | ||| |
---aatgatattttgagctatccagctgggctg-aggagaaagtaaatttgaacatatttttctgttcaaaatgattctagttcagatttatctaatt-ttgcagATTGCGGATTTCTGGAAAGAAGCTCTGATCCTAAGCTCACTCCATCATCCAAATGTGGTTTCATTTTATGGTGTAGTTCGTGATGGTCCAGATGGAAGCT
upper sequence: Vv11s0052g01480.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G039106_T02 (Zea mays), 3'ss of exon 2
-gagaataattttgcaacttcagtgttctgctgtagttcattaccaattacacttgcttcagtttgcattgactgtttgtcta-tccatcttgccgttacagATTGCGGATTTCTGGAAGGAGGCTTTGATATTGAGTTCATTACATCATCCAAATGTCGTTTCCTTTTATGGTATAGTTCGTGATGGCCCTGGTGGCTCTT
|| |||| |||| | | | |||| | | | || ||||||||| | ||| | | || | |||| || ||||| ||||||||||||| || ||| |||| | || ||| | |||||||||||||| ||| | ||||||||| ||||||||||||| || | ||| |
tgaaaata--tttggaggtattaaaatgggctgaggagagtaaatttgaacttatgcttcagtgcaaaatgattctagttcagctttatctaaattttgcagATCACGGATTTCTGGAAAGAAGCTCTGATCCTAAGCTCACTTCATCATCCAAATGTGGTTGCATTTTATGGTGTAGTTCGTGATGGTCCAGATGGAAGCT
upper sequence: Vv11s0052g01480.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA13G01190.2 (Glycine max), 3'ss of exon 6
---gagaataattttgcaacttcagtgttctgc-tgtagttcattaccaattacacttgcttcagtttgcattgactgtttgtctatccatcttgccgttacagATTGCGGATTTCTGGAAGGAGGCTTTGATATTGAGTTCATTACATCATCCAAATGTCGTTTCCTTTTATGGTATAGTTCGTGATGGCCCTGGTGGCTCTT
|| | | | ||| | | | | ||||| ||| || || ||| || | || || | || | ||| || ||||| | ||||||||||||||||| ||||| ||||||||||| |||||||||||||| || ||||||||||| || |||||||||||||| | ||| ||||
aagaggagtgaaatgacaaataaaaaggcttaaatgtagcatatttgaaa---catttg-ttagatacccaactctagtgatttcattctggttgttgtcccagATCACAGATTTCTGGAAGGAGGCGTTGATGTTGAGTTCATTGCATCATCCAAATGTTGTCTCCTTTTATGGCATTGTTCGTGATGGCCCCGATGGTTCTT
upper sequence: Vv11s0052g01480.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA17G07320.1 (Glycine max), 3'ss of exon 9
-gagaataattttgcaacttcagtgttctgc-tgtagttcattaccaattacacttgcttcagtttgcattg-actgtttgtctatccatcttgccgttacagATTGCGGATTTCTGGAAGGAGGCTTTGATATTGAGTTCATTACATCATCCAAATGTCGTTTCCTTTTATGGTATAGTTCGTGATGGCCCTGGTGGCTCTT
|| | | | ||| | | | | ||| | ||| || || ||| | | | | | || | || | ||| || ||||| || || |||||||||||||| ||||| ||||||||||| |||||||||||||| || ||||||||||| || |||||||||||||| | ||| ||||
aaggagtgaaatgacaagtaaaaaggcttaaatgtggcatatttgaaa---catttgttagatccccaactctatagtgatttcattctggttgttgtcccagATCGCAGACTTCTGGAAGGAGGCATTGATGTTGAGTTCATTGCATCATCCAAATGTTGTCTCCTTTTATGGCATTGTTCGTGATGGCCCCGATGGTTCTT
upper sequence: Vv11s0052g01480.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT5G57610.1 (Arabidopsis thaliana), 3'ss of exon 4
gagaataattttgcaacttcagtgttctgctgtagttcat-taccaattacacttgcttcagtttgcattgactgtttgtctatccatcttgccgttacagATTGCGGATTTCTGGAAGGAGGCTTTGATATTGAGTTCATTACATCATCCAAATGTCGTTTCCTTTTATGGTATAGTTCGTGATGGCCCTGGTGGCTCTT
| | ||||| ||| | | | | || | || | || || | | || ||| | | | | ||| || ||| || ||| ||||| | ||||| ||||| || || || ||||||| ||||| |||||||||||||| || || || ||||| |||||||||||||| |||| ||| |||
--gtaaaatttcattcctttattat-caattgaatttaacatattgatcaa---cgtttaagtctagtataattcttttactgcttttct-gctgttgcagATAGAAGATTTTTGGAAAGAAGCCCTGTTATTGAGCTCATTGCATCATCCAAATGTTGTGTCGTTCTATGGGATAGTTCGTGATGGTCCTGATGGTTCTC
upper sequence: Vv11s0052g01480.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: PP1S66_220V6.1 (Physcomitrella patens), 3'ss of exon 4
-------------------------------------------------------gagaataattttgcaacttcagtgttctgctgtagttcattaccaattacacttgctt-cagtttgcattgactgtttgtctat----ccatcttgc---cgttacagATTGCGGATTTCTGGAAGGAGGCTTTGATATTGAGTTCATTACATCATCCAAATGTCGTTTCCTTTTATGGTATAGTTCGTGATGGCCCTGGTGGCTCTT
||| |||| | | || | | | || | ||| | | | | |||||||| ||| | |||| | ||| ||| |||||||| ||||| |||| ||||| | | ||||||| ||||||||||| ||||| ||| |||||||||| |||||||||| || ||||| || |
gtatgatagtcgggtgtattctagtggatctctgatatatggcttaacttacaaattgaacgtctttg-acttagggtctacctttacagagtgtattcaaatgtataggtatatcgtttgcatgtact-tctgtcagtaatgtggagttgtgtttgttgcagATTGCTGATTTTTGGAGAGAGGCATGCACATTGAGTCAGTTACATCATCCTAATGTGGTTGCCTTTTATGGAGTAGTTCGTGACGGTCCTGGAGGGACAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attacacttgcttcagtttgcattgactgtttgtctatccatcttgccgttacagATTGCGGATTTCTGGAAGGAGGCTTTGATATTGAGTTCATTACATCATCCAAATGTCGTTTCCTTTTATGGTATAGTTCGTGATGGCCCTGGTGGCTCTT
cattgac putative branch site (score: 3)
tcttgcc putative PPT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gagaataattttgcaacttcagtgttctgctgtagttcattaccaattacacttgcttcagtttgcattgactgtttgtctatccatcttgccgttacagATTGCGGATTTCTGGAAGGAGGCTTTGATATTGAGTTCATTACATCATCCAAATGTCGTTTCCTTTTATGGTATAGTTCGTGATGGCCCTGGTGGCTCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
-agaataa
- - - - - - -caacttc
- - - - - - - - - - - - -tctgctg
- - - - - - - - - - - - - - - - - - -cattacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcattg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgtttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atccatc