Sequence
atgc intronic sequence ATGC exonic sequence...ccattatcatttatctcctgttttttgtgatccttatgcttttagtttagttttggaagctacagtagttaccgggtacttactttctgctccaatgcagTGATGTTGTTGAGATGGCAAGCTATGCACCACTTTTTGTGAATTCCAATGACAGGAC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv08s0040g00320.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: LOC_Os12g03470.2 (Oryza sativa), 3'ss of exon 14
----------------------------------ccattatcatttatctcctgttttttgtgatccttatgcttttagtttagttt--tggaagctacagt-agttaccgg--gtacttactttctgctccaatgcagTGATGTTGTTGAGATGGCAAGCTATGCACCACTTTTTGTGAATTCCAATGACAGGAC
| | | ||| | | | | | | | || | |||| | | | | | | || | || || ||| | ||| || | | ||||||||||||||| |||||||||| ||||||||||| || ||||| |||||| ||
gttatctttccttgaaacaatcttttctttccgggtcgtgtgacagatcacatttgagctttcctgcgtagggctttattaagatctactaacaaatgcaatgagatatttactgtaacttcttgttggttctttgcagTGATGTTGTTCAGATGGCAAGTTATGCACCACTGTTCGTGAACAACAATGATCAAAC
upper sequence: Vv08s0040g00320.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: LOC_Os12g03530.1 (Oryza sativa), 3'ss of exon 12
ccattatcatttatctcctgttttttgtgatccttat--gcttttagtttagttttggaagctacagtagttaccgggtacttactttctgctccaatgcagTGATGTTGTTGAGATGGCAAGCTATGCACCACTTTTTGTGAATTCCAATGACAGGAC
|| || || || | |||| | ||| | || | | | | || | || || | ||| | ||||||||||||||| |||||||||| ||||||||||| || || ||| ||||||||| ||
acaagataatgaataatacacgtattgtaaatattaatagtgagcagcaagaatactctatcatgaataaattaaaagtg--tatgtcctgtttatctgcagTGATGTTGTTCAGATGGCAAGTTATGCACCACTCTTCGTAAATGACAATGACAGCAC
upper sequence: Vv08s0040g00320.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: LOC_Os11g03730.3 (Oryza sativa), 3'ss of exon 14
-------------------------------------------ccattatcatttatctcctgttttttgtgatccttatgcttttagtttagttttggaagctacagtagttaccgggtacttactttctgctccaatgcagTGATGTTGTTGAGATGGCAAGCTATGCACCACTTTTTGTGAATTCCAATGACAGGAC
| | ||||| | | | || ||| || | || | | || ||| | | | ||| | ||| || | | ||||||||||||||| |||||||||| ||||||||||| || ||||| |||||| ||
gtgatctttccttgaaacaatcttttctttctgggtcttgtgacagatcacatttgagctttcctctgggtagggcttta--ttaagatctactaacaaatgcaacaagatattcattgtaacttcttgttggttctttgcagTGATGTTGTTCAGATGGCAAGTTATGCACCACTCTTCGTGAACAACAATGATCAAAC
upper sequence: Vv08s0040g00320.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: LOC_Os11g03780.1 (Oryza sativa), 3'ss of exon 14
-ccattatcatttatctcctgttttttgtgatccttatgcttttagtttagttttggaagctacagtagttaccgggtacttactttc-tgctccaatgcagTGATGTTGTTGAGATGGCAAGCTATGCACCACTTTTTGTGAATTCCAATGACAGGAC
|| || | | | | | || | || || || || | | | || | | | | || || || || | | ||||||||| ||||| ||||||||||||||||||| || || || ||| ||||||| | ||
tacaagataacatgtacac-atgttgta-aatactaatactgagcagcaaaaatactctccatcatgaataaattaaaagtttctgtcatgtttctttgcagTGATCTTGTTCAGATGGCAAGCTATGCACCGCTCTTCGTAAATGACAATGACCGCAC
upper sequence: Vv08s0040g00320.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: GRMZM2G097277_T01 (Zea mays), 3'ss of exon 13
ccattatcatttatct-cctgttttttgtgatccttatgcttttagtttagttttggaagctacagtagttaccgggtacttactttctgctccaatgcagTGATGTTGTTGAGATGGCAAGCTATGCACCACTTTTTGTGAATTCCAATGACAGGAC
||| | | | | || ||| || | || | | | | | || | | | || || ||| | | || || | ||||||||||| |||||||||||||||| |||||| |||||||| ||| |||||| | |
--gttagctgtagtgtacccgttcttcctcattttagagttctg---ccaaaattaaagcatgttgcagatata----actgtttgtttgttctactgcagTGATGTGGTTGAGATGGCAAGCTGTGCACCCCTTTTTGTAAATGACAATGATCGCAG
upper sequence: Vv08s0040g00320.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: GLYMA03G27460.2 (Glycine max), 3'ss of exon 13
ccattatcatttatctcctgttttttgtgatccttatgcttttagtttagttttggaagctaca-gtagttaccgggtacttactttctgctccaatgcagTGATGTTGTTGAGATGGCAAGCTATGCACCACTTTTTGTGAATTCCAATGACAGGAC
| | | | || | || | | || || || ||| | | || ||| | ||| | | | ||| || |||||||||||| | | ||||| |||||||| ||||||||||| ||| ||||||| ||||
-tttggttcctagtagtatgaaatctgagtttctaatctagttcacttaatagcatcattagcatgtactcaccattttcatttttttctttctggtgcagTGATGTTATCCAAATGGCCAGCTATGCTCCACTTTTTGTTAATGCCAATGATAGGAG
upper sequence: Vv08s0040g00320.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: GLYMA19G30450.1 (Glycine max), 3'ss of exon 14
--ccattatcatttatctcctgttttttgtgatccttatgcttttagtttagttttggaagctaca-gtagttaccgggtacttactttctgctccaatgcagTGATGTTGTTGAGATGGCAAGCTATGCACCACTTTTTGTGAATTCCAATGACAGGAC
||| || | | | | || ||| | | || | | ||||| | || ||| | || | | | | ||| | || |||||||||||| | | ||||| |||||||| ||||||||||| ||| ||||||| ||||
cgtttctattcttggttcctagcagtatgaaatc--tgagtttctgatctagttcacttaatagcatgtactcactgttttcattttttat-ttctggtgcagTGATGTTATCCAAATGGCCAGCTATGCTCCACTTTTTGTTAATGCCAATGATAGGAGMapped 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|33406071|gb|CF211698.1|CF211698EST: TTGGCAGCATTGGCTGAAGCTGCATTCCTCATTGGGGTGGAAAAGAACAG TAATGTTGTTGAGATGGCAAGCTATGCACCACTTTTTGTGAATTCCAATGA
genomic: TTGGCAGCATTGGCTGAAGCTGCATTCCTCATTGGGGTGGAAAAGAACAGgtctgctctg ... tccaatgcagTGATGTTGTTGAGATGGCAAGCTATGCACCACTTTTTGTGAATTCCAATGA
EST:
gi|161713404|gb|FC062796.1|FC062796EST: TTGGCAGCATTGGCTGAAGCTGCATTCCTCATTGGGGTGGAAAAGAACAG TGATGTTGTTGAGATGGCAAGCTATGCACCACTTTTTGTGAATTCCA-TGA
genomic: TTGGCAGCATTGGCTGAAGCTGCATTCCTCATTGGGGTGGAAAAGAACAGgtctgctctg ... tccaatgcagTGATGTTGTTGAGATGGCAAGCTATGCACCACTTTTTGTGAATTCCAATGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttagttttggaagctacagtagttaccgggtacttactttctgctccaatgcagTGATGTTGTTGAGATGGCAAGCTATGCACCACTTTTTGTGAATTCCAATGACAGGAC
tacttac putative branch site (score: 1)
cttactttctgctcc CT-rich tract
ttacttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ccattatcatttatctcctgttttttgtgatccttatgcttttagtttagttttggaagctacagtagttaccgggtacttactttctgctccaatgcagTGATGTTGTTGAGATGGCAAGCTATGCACCACTTTTTGTGAATTCCAATGACAGGAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - ctcctgt
- - - - - - - - - - - - - - - - cttatgc