Sequence
atgc intronic sequence ATGC exonic sequence...agggtgccaaatgatgaataatttaggattcaaaaaccaaatgtaaggttagtgattttgtgaaatttggatctcttttatccttgactgtgattacaagACAAATGTGATGGGCACCCTGAACATGTTGGGCCTTGCAAAGAGGATTGGGGCAAGGTTTTTGCTCACAAGTACAAGTGAAGTTTATGGTGACCCCCTTG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv08s0040g02710.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os01g62020.1 (Oryza sativa), 3'ss of exon 1
-agggtgccaaatgatgaataatttaggattcaaaaacca-aatgtaa--ggttagtgattttgtgaaatttggatctcttttatccttgactgtgattacaagACAAATGTGATGGGCACCCTGAACATGTTGGGCCTTGCAAAGAGGATTGGGGCAAGGTTTTTGCTCACAAGTACAAGTGAAGTTTATGGTGACCCCCTTG
| | | | || || | |||| | | ||| ||| | || | ||| | | | | ||| | ||| || | |||||||||| ||||| ||||| ||| |||| |||||||| || |||||| | ||||| |||||||| ||||| || || ||||||||||||||||| || || |
catgtttttttgcaacttattatgttattttcactatttacaatataatcatgtgttgcatctgtatattatcaaa-tctgggtttcttaacaattattacAAGACCAATGTCATGGGAACCTTGAATATGTTGGGTCTGGCAAAGCGAATTGGTGCAAGGTTCTTGCTAACTAGCACAAGTGAAGTTTATGGAGATCCAC---
upper sequence: Vv08s0040g02710.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os03g17230.1 (Oryza sativa), 3'ss of exon 1
----agggtgccaaatgatgaataatttaggattcaaaaaccaaatgtaaggttagtgattttgtgaaatttggatctcttttatccttgactgtgat--tacaagACAAATGTGATGGGCACCCTGAACATGTTGGGCCTTGCAAAGAGGATTGGGGCAAGGTTTTTGCTCACAAGTACAAGTGAAGTTTATGGTGACCCCCTTG
||||| | || |||| | | || |||| | | ||| | | | || | | || ||| | ||||| || |||||||||||||||||||| ||| |||||||| |||| | ||||||||| | || || |||| || | || ||||| ||||| || || ||||| || |
gaatcttgtgcctgcggttg--ccattt-gcctggaagaacctgaaattttgttccagtcctatttttccttataaattttggttccctaactgttatagtacAAGACAAATGTGATGGGGACCTTGAACATGCTGGGATTGGCAAAGAGGGTGGGAGCCCGGTTCTTATTGACCAGTACCAGTGAGGTGTACGGTGATCCTC---
upper sequence: Vv08s0040g02710.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G359234_T03 (Zea mays), 3'ss of exon 1
----agggtgccaaatgatgaataatttagg-attcaaaaaccaaatgtaaggt-tagtgattttgtg--aaatttggatctcttttatccttgactgtgattacaagACAAATGTGATGGGCACCCTGAACATGTTGGGCCTTGCAAAGAGGATTGGGGCAAGGTTTTTGCTCACAAGTACAAGTGAAGTTTATGGTGACCCCCTTG
| | |||| | || | || | ||||| | ||| || | ||| | | |||||| |||||||| |||| | ||| |||||||||||||| ||||| || |||| |||||||| || || ||| | ||||| |||||||||||| | || || |||||||||||||||||||| || ||||
aaggatgtcgccattttttgcagcatgtgtccattcagtatccatatagatggtgtgtttcttttgtctcgaatttggacttcttaacactttg--------tacaagACAAATGTCATGGGAACTTTGAATATGTTGGGTCTGGCGAAGCGAATTGGTGCAAGGTTTTTGTTGACTAGCACAAGTGAAGTTTATGGTGATCCGCTTG
upper sequence: Vv08s0040g02710.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G370048_T01 (Zea mays), 3'ss of exon 2
----agggtgccaaatgatgaataatttaggattcaaaaaccaaatgtaaggttagtgattttgtgaaatttggatctcttttatccttgactgtgattacaagACAAATGTGATGGGCACCCTGAACATGTTGGGCCTTGCAAAGAGGATTGGGGCAAGGTTTTTGCTCACAAGTACAAGTGAAGTTTATGGTGACCCCCTTG
| | ||| | ||| | || ||| | ||| | ||| ||| | | | | | | ||| || | |||||||||||||| ||||| || |||| |||||||| || |||||| | |||| |||||||||||| | || || |||||||||||||||||||| || |
atcaatcccctccaatccgtatggattgaaaataaccgaacaagccctaaatgttttgagtttcttttgtctaaaatttggac-ttcttaacactttgtacAAGACAAATGTCATGGGAACTTTGAATATGTTGGGTCTGGCAAAGCGAGTTGGTGCAAGGTTTTTGTTGACTAGCACAAGTGAAGTTTATGGTGATCCAC---
upper sequence: Vv08s0040g02710.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G359234_T01 (Zea mays), 3'ss of exon 1
-------agggtgccaaatgatgaataatttagg-attcaaaaaccaaatgtaaggt-tagtgattttgtg--aaatttggatctcttttatccttgactgtgattacaagACAAATGTGATGGGCACCCTGAACATGTTGGGCCTTGCAAAGAGGATTGGGGCAAGGTTTTTGCTCACAAGTACAAGTGAAGTTTATGGTGACCCCCTTG
| | |||| | || | || | ||||| | ||| || | ||| | | |||||| |||||||| |||| | ||| |||||||||||||| ||||| || |||| |||||||| || || ||| | ||||| |||||||||||| | || || |||||||||||||||||||| || |
gggaaggatgtcgccattttttgcagcatgtgtccattcagtatccatatagatggtgtgtttcttttgtctcgaatttggacttcttaacactttg--------tacAAGACAAATGTCATGGGAACTTTGAATATGTTGGGTCTGGCGAAGCGAATTGGTGCAAGGTTTTTGTTGACTAGCACAAGTGAAGTTTATGGTGATCCGC---
upper sequence: Vv08s0040g02710.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G347717_T01 (Zea mays), 3'ss of exon 1
-----agggtgccaa-atgatgaataatttaggattcaaaaaccaaatgtaaggttagtgattttgtgaaatttggatctcttttatccttgactgtgattacaagACAAATGTGATGGGCACCCTGAACATGTTGGGCCTTGCAAAGAGGATTGGGGCAAGGTTTTTGCTCACAAGTACAAGTGAAGTTTATGGTGACCCCCTTG
|||| || ||||| | || | | | | | || || |||| | || || || | | ||| || |||||||||||||| ||||| ||| |||| ||| | || || || |||||| ||||||| |||| ||| | || ||||| |||||||| |||||||| || ||||
gtagttttgtgcttgcgtggggaatagcctgtattt--acatctgtttattttgtctgttttttttttt--cttcaattgtttctttaaccaactatg--tacaagACAAATGTCATGGGGACCTTGAATATGCTTGGACTGGCTAAGAGGGTTGGGGCTCGGTTCTTGTTGACTAGTACCAGTGAAGTGTATGGTGATCCTCTTG
upper sequence: Vv08s0040g02710.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G347717_T03 (Zea mays), 3'ss of exon 1
--------agggtgccaa-atgatgaataatttaggattcaaaaaccaaatgtaaggttagtgattttgtgaaatttggatctcttttatccttgactgtgattacaagACAAATGTGATGGGCACCCTGAACATGTTGGGCCTTGCAAAGAGGATTGGGGCAAGGTTTTTGCTCACAAGTACAAGTGAAGTTTATGGTGACCCCCTTG
|||| || ||||| | || | | | | | || || |||| | || || || | | ||| || |||||||||||||| ||||| ||| |||| ||| | || || || |||||| ||||||| |||| ||| | || ||||| |||||||| |||||||| || |
tttgtagttttgtgcttgcgtggggaatagcctgtattt--acatctgtttattttgtctgttttttttttt--cttcaattgtttctttaaccaactatg--tacAAGACAAATGTCATGGGGACCTTGAATATGCTTGGACTGGCTAAGAGGGTTGGGGCTCGGTTCTTGTTGACTAGTACCAGTGAAGTGTATGGTGATCCTC---
upper sequence: Vv08s0040g02710.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA10G05260.1 (Glycine max), 3'ss of exon 1
--------------agggtgccaaatgatgaataatttaggattcaaaaaccaaatgtaaggtta-gtgattttgtgaaatttg----gatctcttttatccttgactgt--gattacaagACAAATGTGATGGGCACCCTGAACATGTTGGGCCTTGCAAAGAGGATTGGGGCAAGGTTTTTGCTCACAAGTACAAGTGAAGTTTATGGTGACCCCCTTG
|| | || | ||| | | || || ||| | | || || ||||| | |||| || ||| | |||||| | ||| | ||||||||| |||||||||||||| || |||||| | |||||||| ||||| |||||||| |||||| |||| || ||||| ||||| ||||| ||||| ||
atatccttcctctctatgttctaactc-tgactcgccgtgtttttaagttccagctctcttttttcgtaattttttatgttttgtgttgaattctgtgatccttaattgttggcttacAAGACGAATGTGATGGGCACGCTTAACATGCTTGGCCTTGCGAAGAGAATTGGGGCTAGGTTTCTGCTTACTAGTACTAGTGAGGTTTACGGTGATCCGT---
upper sequence: Vv08s0040g02710.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA13G19640.1 (Glycine max), 3'ss of exon 1
-------------agggtgccaaatgatgaataatttaggattcaaaaaccaa--atgtaaggttagtgatttt-gtgaaatttggatctcttttatccttgactgt--gattacaagACAAATGTGATGGGCACCCTGAACATGTTGGGCCTTGCAAAGAGGATTGGGGCAAGGTTTTTGCTCACAAGTACAAGTGAAGTTTATGGTGACCCCCTTG
|| | || | | | || || | || | || || ||||| | | || ||| | |||||| | | | | ||||||||| |||||||||||||| || |||||| | |||||||| ||| | |||||||| |||||| |||| || ||||| ||||| ||||| ||||| || |
atatccttgtctcgatgttctaactctaactcagcgttttttttaagttctaataactcttttttcgtaatttttattttgcgttgagttctgtgatccttaattattagtttacAAGACGAATGTGATGGGCACGCTTAACATGCTTGGCCTTGCGAAGCGAATTGGGGCTAGGTTTCTGCTTACTAGTACTAGTGAGGTTTACGGTGATCCGC---
upper sequence: Vv08s0040g02710.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT3G53520.1 (Arabidopsis thaliana), 3'ss of exon 1
agggtgcca-aatgatgaataatttaggattcaaaaaccaaatgtaaggttagtgattttgtgaaatttggatctcttttatccttgactgtgatt--acaagACAAATGTGATGGGCACCCTGAACATGTTGGGCCTTGCAAAGAGGATTGGGGCAAGGTTTTTGCTCACAAGTACAAGTGAAGTTTATGGTGACCCCCTTG
| || | | || | || | ||||| || ||| | | || ||| || |||||| || | || ||||||||||||| |||||||| || || |||||||| ||||||||||| |||||||||||||| ||||||| || ||||||||||| ||||| || ||||
caattattgtgatatttcgtgatgaaatgtttccattgggaatgtgtttttctctattgttgatatgatgattctggttgatccttaaccatagttttacAAGACAAATGTAATGGGCACTCTCAATATGTTGGGTCTTGCAAAGAGAGTTGGGGCAAGGTTTCTGCTCACCAGCACAAGTGAAGTCTATGGAGATCCCC---
upper sequence: Vv08s0040g02710.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT3G53520.4 (Arabidopsis thaliana), 3'ss of exon 1
------agggtgcca-aatgatgaataatttaggattcaaaaaccaaatgtaaggttagtgattttgtgaaatttggatctcttttatccttgactgtgat--tacaagACAAATGTGATGGGCACCCTGAACATGTTGGGCCTTGCAAAGAGGATTGGGGCAAGGTTTTTGCTCACAAGTACAAGTGAAGTTTATGGTGACCCCCTTG
| || | | || | || | ||||| || ||| | | || ||| || |||||| || | | |||||||||||||| |||||||| || || |||||||| ||||||||||| |||||||||||||| ||||||| || ||||||||||| ||||| |
ctcttacaattattgtgatatttcgtgatgaaatgtttccattgggaatgtgtttttctctattgttgatatgatgattctggttgatccttaaccatagTTTTACAAGACAAATGTAATGGGCACTCTCAATATGTTGGGTCTTGCAAAGAGAGTTGGGGCAAGGTTTCTGCTCACCAGCACAAGTGAAGTCTATGGAG---------Mapped 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|30128347|gb|CB913686.1|CB913686EST: CAGTTCATTACAAGTATAATCCTGTTAAAACAA-T-TA-----A--G--- ACAAATGTGATGGGCACCCTGAACATGTTGGGCCTTGCAAAGAGGATTGGG
genomic: CAGTTCATTACAAGTATAATCCTGTTAAAACAATTATATCCTTATTGATTgttatgttgg ... tgattacaagACAAATGTGATGGGCACCCTGAACATGTTGGGCCTTGCAAAGAGGATTGGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aggttagtgattttgtgaaatttggatctcttttatccttgactgtgattacaagACAAATGTGATGGGCACCCTGAACATGTTGGGCCTTGCAAAGAGGATTGGGGCAAGGTTTTTGCTCACAAGTACAAGTGAAGTTTATGGTGACCCCCTTG
ccttgac putative branch site (score: 4)
attttgtgaaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agggtgccaaatgatgaataatttaggattcaaaaaccaaatgtaaggttagtgattttgtgaaatttggatctcttttatccttgactgtgattacaagACAAATGTGATGGGCACCCTGAACATGTTGGGCCTTGCAAAGAGGATTGGGGCAAGGTTTTTGCTCACAAGTACAAGTGAAGTTTATGGTGACCCCCTTG
- - - ccaaatg
- - - - - - -atgaataa
- - - - - - - - - - - - - - - - -aaaccaa