Sequence
atgc intronic sequence ATGC exonic sequencegtaggataaataaatcttctgtcatgcttggttttaacttctattcttgaatctttaggtttcagactctccattgctttaattgtttttgattttagtgctcttgtgtccatgtagGAGCCCAAAAACTTGCACAAATACGTGAGAATAGCAACTTTTTCAGGTCAGAACTGCAGAGCATGGGTTTTGAGGTTCTTGGGGATAATGACTCTCCAGT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv14s0068g01300.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os11g31640.1 (Oryza sativa), 3'ss of exon 9
gtaggataaataaatcttctgtcatgcttggttttaacttctattcttgaatctttaggtttcagactctccattgctttaattgtttttgattttagtgctcttgtgtccatgtagGAGCCCAAAAACTTGCACAAATACGTGAGAATAGCAACTTTTTCAGGTCAGAACTGCAGAGCATGGGTTTTGAGGTTCTTGGGGATAATGACTCTCCAGT
| | ||| | | ||||| | | || | || | | | || | | || |||| || || ||||| || | | |||| || ||| ||||| |||||||||| || |||||||| ||||| || || |||||||| || ||| ||||||||||||||||| || || ||||||||||||||
-------gtactagccttttcttctgcttcgaccctttcaatgcgctgcaggctatccatgtaagttttact-----ttcaattcttatttattttggt--tttgatgtct-tgcagGTGCCCAGAAACTTGCACGCATCCGTGAGAACAGCAATTTCTTTAGGTCAGAGCTCAAGAAGATGGGTTTTGAGGTTCTCGGAGACAATGACTCTCCAGT
upper sequence: Vv14s0068g01300.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G055854_T01 (Zea mays), 3'ss of exon 7
------------------------------------------gtaggataaataaatcttctgtcatgcttggttttaacttctattcttgaatctttaggtttcagactctccattgctttaattgtttt---tgattttagtgctcttgtg-tcca-tgtagGAGCCCAAAAACTTGCACAAATACGTGAGAATAGCAACTTTTTCAGGTCAGAACTGCAGAGCATGGGTTTTGAGGTTCTTGGGGATAATGACTCTCCAGT
| || | | ||| ||| | | | | || | || | || | | || | || | || || || | ||| | | |||||| | | || ||| |||||||||||||| | || || |||||||| || || ||||||||||| || ||| |||||||||||||||||||| || ||||||||||| ||
gtactaaaccagtttctttaacactttttgcccttttcatttgcagc-tgtgttaatgttcgattaaa-taattcttttttccttgtgatgtactgaagGTGCCCAAAAACTTGCTCGCGGATGTTCGATTAAATAATTCTTTTTTCCTTGTGATGTACTGAAGGTGCCCAAAAACTTGCTCGCATCCGCGAGAATAGTAATTTCTTCAGGTCAGAGCTCAAGAAGATGGGTTTTGAGGTTCTTGGTGACAATGACTCTCCTGT
upper sequence: Vv14s0068g01300.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G357734_T03 (Zea mays), 3'ss of exon 14
gtaggataaataaatcttctgtcatgcttggttttaacttctattcttgaatctttaggtttcagactctccattgctttaattgtttttgattttagtgctcttgtgtccatgtagGAGCCCAAAAACTTGCACAAATACGTGAGAATAGCAACTTTTTCAGGTCAGAACTGCAGAGCATGGGTTTTGAGGTTCTTGGGGATAATGACTCTCCAGT
| | | || | || |||||| || ||| ||| || ||| | || | | | | | |||| | || || || ||| |||||||||||||| | || || |||||||| || || ||||||||||| || ||| |||||||||||||||||||| || ||||||||||| ||
-----------aggtactaaacca-gttt--ctttaacac---tttttgcccttttcatttgcagctatgttaatgttcgattaaataattctttttttccttgtgatgtactgaagGTGCCCAAAAACTTGCTCGCATCCGCGAGAATAGTAATTTCTTCAGGTCAGAGCTCAAGAAGATGGGTTTTGAGGTTCTTGGTGACAATGACTCTCCTGT
upper sequence: Vv14s0068g01300.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G137556_T01 (Zea mays), 3'ss of exon 5
gtaggataaataaatcttctgtcatgcttggttttaacttctattcttgaatctttaggtttcagactctccattgctttaattgtttttgattttagtgctcttgtgtccatgtagGAGCCCAAAAACTTGCACAAATACGTGAGAATAGCAACTTTTTCAGGTCAGAACTGCAGAGCATGGGTTTTGAGGTTCTTGGGGATAATGACTCTCCAGT
| | | || | || |||||| || ||| ||| || || | || | | | | | |||| | || || || ||| |||||||||||||| || || || |||||||| || || ||||||||||| || ||| |||| ||||||||||||||| || ||||||||||| ||
-----------aggtactaaacca-gttt--ctttaacac---tttttgcccttttcatttgtagttgtgttaatgttcgattaaataattctttttttccttgtgatgtactgaagGTGCCCAAAAACTTGCTCACATCCGCGAGAATAGTAATTTCTTCAGGTCAGAGCTCAAGAAGATGGTTTTTGAGGTTCTTGGTGACAATGACTCTCCTGT
upper sequence: Vv14s0068g01300.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G067257_T01 (Zea mays), 3'ss of exon 10
gtaggataaataaatcttctgtcatgcttggttttaacttctattcttgaatctttaggtttcagactctccattgctttaattgtttttgattttagtgctcttgtgtccatgtagGAGCCCAAAAACTTGCACAAATACGTGAGAATAGCAACTTTTTCAGGTCAGAACTGCAGAGCATGGGTTTTGAGGTTCTTGGGGATAATGACTCTCCAGT
| | | || | || |||||| || ||| ||| || ||| | || | | | | | |||| | || || || ||| |||||||||||||| | || || |||||||| || || ||||||||||| || ||| |||||||||||||||||||| || ||||||||||| ||
-----------aggtactaaacca-gttt--ctttaacac---tttttgcccttttcatttgcagctgtgttaatgttcgattaaataattctttttttccttgtgatgtactgaagGTGCCCAAAAACTTGCTCGCATCCGCGAGAATAGTAATTTCTTCAGGTCAGAGCTCAAGAAGATGGGTTTTGAGGTTCTTGGTGACAATGACTCTCCTGT
upper sequence: Vv14s0068g01300.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM5G891276_T01 (Zea mays), 3'ss of exon 6
gtaggataaataaatcttctgtcatgcttggttttaacttctattcttgaatctttaggtttcagactctccattgctttaattgtttttgattttagtgctcttgtgtccatgtagGAGCCCAAAAACTTGCACAAATACGTGAGAATAGCAACTTTTTCAGGTCAGAACTGCAGAGCATGGGTTTTGAGGTTCTTGGGGATAATGACTCTCCAGT
| | | |||| | || ||| ||| || ||| | || || | | | | ||||| | | ||| | || ||| |||||||||||||| | || | |||||||| || || ||||||||||| || ||| |||||||||||||||||||| ||||||||||||| ||
------------------gtactaaacc-agtttctttaacactttttgcccttttcatttgcagttgtgttaatgtttgattaaataattattttttccttgtgatgtac-tgaagGTGCCCAAAAACTTGCTCGCATCTGCGAGAATAGTAATTTCTTCAGGTCAGAGCTCAAGAAGATGGGTTTTGAGGTTCTTGGTGATAATGACTCTCATGT
upper sequence: Vv14s0068g01300.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G142030_T01 (Zea mays), 3'ss of exon 9
gtaggataaataaatcttctgtcatgcttggttttaacttctattcttgaatctttaggtttcagactctccattgct---ttaattgtttttgattttagtgctcttgtgtccatgtagGAGCCCAAAAACTTGCACAAATACGTGAGAATAGCAACTTTTTCAGGTCAGAACTGCAGAGCATGGGTTTTGAGGTTCTTGGGGATAATGACTCTCCAGT
| | || || || |||| |||| || ||| | || ||| | || | |||| ||||||| || | ||| | | | || ||| |||||||||||||||| || |||||||| | || || |||||||| ||||| ||| |||||||||||||||||||| || ||||| ||||| ||
-------------gtactaaaccagctttttttaacacttttatttgtgcccttttcgtttgcagctgtgttagtgttcaattaaatgtttttttttcttgtgat---atat---tgaagGTGCCCAAAAACTTGCACGCATCCGTGAGAACGGTAATTTCTTCAGGTCCGAACTCAAGAAGATGGGTTTTGAGGTTCTTGGCGACAATGATTCTCCTGT
upper sequence: Vv14s0068g01300.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G152888_T01 (Zea mays), 3'ss of exon 9
gtaggataaataaatcttctgtcatgcttggttttaacttctattcttgaatctttaggtttcagactctccattgctttaattgtttttgattttagtgctcttgtgtccatgtagGAGCCCAAAAACTTGCACAAATACGTGAGAATAGCAACTTTTTCAGGTCAGAACTGCAGAGCATGGGTTTTGAGGTTCTTGGGGATAATGACTCTCCAGT
| | || | ||||| | | ||| ||| | | | ||| | || | | | || ||| | | | ||||| || | || || | ||| |||||||||||||| | || || |||||||| || || || |||||||| || ||| |||||||||||||||||||| || ||||||||||| ||
---gtactaaaccagcttctttaacactt---tttgcccttttcatttgcagctgtg-----ctaatgttcgattaaataattcttttttccttgtgatgtact---------gaagGTGCCCAAAAACTTGCTCGCATCCGCGAGAATAGTAATTTCTTTAGGTCAGAGCTCAAGAAGATGGGTTTTGAGGTTCTTGGTGACAATGACTCTCCTGT
upper sequence: Vv14s0068g01300.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G030862_T01 (Zea mays), 3'ss of exon 8
gtaggataaataaatcttctgtcatgcttggttttaacttctattcttgaatctttaggtttcagactctccattgctttaattgtttttgattttagtgctcttgtgtc-catgtagGAGCCCAAAAACTTGCACAAATACGTGAGAATAGCAACTTTTTCAGGTCAGAACTGCAGAGCATGGGTTTTGAGGTTCTTGGGGATAATGACTCTCCAGT
| | ||| || | | | | | | | || |||| | || | ||| || ||| |||||||| || | ||||| | || ||| ||||| ||||| || | || |||||||| |||||||| ||||||||||| || ||| ||||| |||||||||||||| || || |||||||| ||
----gtccctccccttttcgttcgcgactatatatgtgtccaa--ctagaataatgttgtactgaataatcctttttttt--ttgtttttttgcttgcttgggatgtgttgcttgcagGTGCCCAGAAACTGGCGCGCATCCGTGAGAACAGCAACTTCTTCAGGTCAGAGCTCAAGAAGATGGGCTTTGAGGTTCTTGGTGACAACGACTCTCCTGT
upper sequence: Vv14s0068g01300.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G370377_T01 (Zea mays), 3'ss of exon 11
------------------------------------------gtaggataaataaatcttctgtcatgcttggttttaacttctattcttgaatctttaggtttcagactctccattgctttaattgtttt---tgattttagtgctcttgtg-tcca-tgtagGAGCCCAAAAACTTGCACAAATACGTGAGAATAGCAACTTTTTCAGGTCAGAACTGCAGAGCATGGGTTTTGAGGTTCTTGGGGATAATGACTCTCCAGT------------------------------------
| || | | ||| ||| | | | | || | || | || | | || | || | || || || | ||| | | |||||| | | || ||| |||||||||||||| | || || | | || ||||||||||| || ||| |||||||||||||||||||| || ||||||||||| ||
gtactaaaccagtttctttaacactttttgcccttttcatttgcagc-tgtgttaatgttcgattaaa-taattcttttttccttgtgatgtactaaaggtgcccaaaaacttgctcgcggatgttcgattaaataattcttttttccttgtgatgtactgaaggtgcccaaaaacttgctcgcatccggctaag-
upper sequence: Vv14s0068g01300.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G157249_T01 (Zea mays), 3'ss of exon 2
gtaggataaataaatcttctgtcatgcttggttttaacttctattcttgaatctttaggtttcagactctccattgctttaattgtttttgattttagtgctcttgtgtccatgtagGAGCCCAAAAACTTGCACAAATACGTGAGAATAGCAACTTTTTCAGGTCAGAACTGCAGAGCATGGGTTTT-GAGGTTCTTGGGGATAATGACTCTCCAGT
|||| | | |||| | | ||| ||| || ||| | | | | | || | | | |||| || || |||| || || | ||| |||||||||||||| | || || |||||||| || || ||||||||||| || ||| ||||||||| ||||||||||| || ||||||||||| |
--gtactaaactagt-ttctttaacacttt-tttcccttttcatttgcagctgtgttaatgttcgattaaataattctttttttccttgtgat----gtact-----------gaagGTGCCCAAAAACTTGCTCGCATCCGCGAGAATAGTAATTTCTTCAGGTCAGAGCTCAAGAAGATGGGTTTTTGAGGTTCTTGGTGACAATGACTCTCCTG-
upper sequence: Vv14s0068g01300.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G010202_T02 (Zea mays), 3'ss of exon 8
gtaggataaataaatcttctgtcatgcttggttttaacttct-attcttgaatctttaggtttcagactctccattgctttaattgtttttgattttagtgctcttgtgtccatgtagGAGCCCAAAAACTTGCACAAATACGTGAGAATAGCAACTTTTTCAGGTCAGAACTGCAGAGCATGGGTTTTGAGGTTCTTGGGGATAATGACTCTCCAGT
| ||| || || |||| | | | | || | | | ||| | || | ||| || | | || | | || | |||| ||| | || || || ||||| || ||||| ||||| || ||| | || || || |||| |||||||||||||||||||| |||||||| || || ||
----------------gtacaacataaagaattccaaattcttacaccttaccagtt---tcttatacttcctgccttgttgaatgtctt--aatgtaacaattgt---tctaattagGGGCCAAGAAGCTCGCTCAAATTCGAGAGAACAGCAATTTCTTCCGCTCGGAGCTTCAGAAAATGGGTTTTGAGGTTCTTGGAGATAATGATTCACCTGT
upper sequence: Vv14s0068g01300.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA02G07250.1 (Glycine max), 3'ss of exon 9
-gtaggataa-ataaatcttctgtcatgcttggttttaacttctattcttgaatctttaggt-------ttcagac--tctccat-tgctttaattgtttttgattttagtgctcttgtgtccatgtagGAGCCCAAAAACTTGCACAAATACGTGAGAATAGCAACTTTTTCAGGTCAGAACTGCAGAGCATGGGTTTTGAGGTTCTTGGGGATAATGACTCTCCAGT
| || | | | | | ||||| | || | || ||| | |||| || | || | | | | | | |||| || | ||| ||| || | || || |||| ||||| |||||||||||||| || ||||||||||||||||| |||||||||||||||| ||||| ||||||||||||||||||||||| ||||||||
gtttggctggcactagttctgctctttgctttgcatttgtattgtttgatgattttttatgtgcatcaatccaaataatattcgtctactttgtttaccgtgcattgaagtaagttttt-tctatatagGTGCCCAGAAACTTGCACAAATTCGAGAGAATAGCAACTTTTTTAGGTCAGAACTGCAGAAGATGGGATTTGAGGTTCTTGGGGATAATGATTCTCCAGT
upper sequence: Vv14s0068g01300.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA16G26210.1 (Glycine max), 3'ss of exon 9
gtaggataaataaatcttctgtcatgcttggttttaacttctattct-tgaatctttaggt-------ttcagac--tctccat-tgctttaattgtttttgattttagtgctcttgtgtccatgtagGAGCCCAAAAACTTGCACAAATACGTGAGAATAGCAACTTTTTCAGGTCAGAACTGCAGAGCATGGGTTTTGAGGTTCTTGGGGATAATGACTCTCCAGT
|| | | ||||| | ||| ||| | || |||| || | |||| || | || | | | ||| | |||| || || ||| ||| |||| || || |||| ||||| |||||||||||||| || || |||||||||||||||||||||||| |||||| ||||| ||||||||||||||||||||||| ||||||||
gtttggctggcactagttctgctct--ttgctttgcatttgtatttgatggttttttacgtgcatcaatccaaataatattcatctactttgtttaccttgcattgaagtaag-ttgtttctatatagGTGCCCAGAAACTTGCACAAATTCGAGAAAATAGCAACTTTTTCAGGTCAGAATTGCAGAAGATGGGATTTGAGGTTCTTGGGGATAATGATTCTCCAGT
upper sequence: Vv14s0068g01300.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AT5G23670.1 (Arabidopsis thaliana), 3'ss of exon 9
gtaggataaataaatcttctgtcatgcttggttttaacttctatt-cttgaatctttaggt----ttcagactctccattgctttaattgtttttgattttagtgctcttgtgt-ccatgtagGAGCCCAAAAACTTGCACAAATACGTGAGAATAGCAACTTTTTCAGGTCAGAACTGCAGAGCATGGGTTTTGAGGTTCTTGGGGATAATGACTCTCCAGT
|| | | || | | || |||| | | ||| || | | | | | ||| || | | | | | ||| | | ||| || ||||| || ||| |||||||||||| |||||||||||| || | || ||||||| ||||| |||||||| ||||| || ||||| || |||||
-----gtactcgattttttttctcaccgtgtcattaattggcctcatttgggtcactgagcacaatctaatcaggtcatgactcataacctaaaaactcccattcttctcaaatactgaacagGGGCACAAAAGCTAGCAAGAATACGTGAGAACAGCAACTTTTTCCGGGCTGAGCTGCAGAAGATGGGATTTGAGGTACTTGGAGACAATGATTCCCCAGTMapped 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|352778117|gb|FQ467170.1|FQ467170EST: AGGTTATTCTTGGAGAGGATGGTTCTTGTAGAG GAGCCCAAAAACTTGCACAAATACGTGAGAATAGCAACTTTTTCAGGTCAG
genomic: AGGTTATTCTTGGAGAGGATGGTTCTTGTAGAGgtaggataaa ... gtccatgtagGAGCCCAAAAACTTGCACAAATACGTGAGAATAGCAACTTTTTCAGGTCAG
EST:
gi|329112275|gb|JG391743.1|JG391743EST: AATTATCTCTGCTATAAAGGTTATTCTTGGAGAGGATGGTTCTTGTAGAG GAGCCCAAAAACTTGCACAAATACGTGAGAATAGCAACTTTTTCAGGTCAG
genomic: AATTATCTCTGCTATAAAGGTTATTCTTGGAGAGGATGGTTCTTGTAGAGgtaggataaa ... gtccatgtagGAGCCCAAAAACTTGCACAAATACGTGAGAATAGCAACTTTTTCAGGTCAG
EST:
gi|352789616|gb|FQ476214.1|FQ476214EST: GTTATTCTGGGAGGGGATGGTTCATGTAGAG GAGCCCAAAAACTTGCACAAATACGTGAGAATAGCAACTTTTTCAGGTCAG
genomic: GTTATTCTTGGAGAGGATGGTTCTTGTAGAGgtaggataaa ... gtccatgtagGAGCCCAAAAACTTGCACAAATACGTGAGAATAGCAACTTTTTCAGGTCAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cagactctccattgctttaattgtttttgattttagtgctcttgtgtccatgtagGAGCCCAAAAACTTGCACAAATACGTGAGAATAGCAACTTTTTCAGGTCAGAACTGCAGAGCATGGGTTTTGAGGTTCTTGGGGATAATGACTCTCCAGT
ttttgat putative branch site (score: 4)
tttaattgtttttgat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaggataaataaatcttctgtcatgcttggttttaacttctattcttgaatctttaggtttcagactctccattgctttaattgtttttgattttagtgctcttgtgtccatgtagGAGCCCAAAAACTTGCACAAATACGTGAGAATAGCAACTTTTTCAGGTCAGAACTGCAGAGCATGGGTTTTGAGGTTCTTGGGGATAATGACTCTCCAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA