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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acatagtgtttgtaaaactgtgtttctatgcatgctttgtattagaatcttaattatgaaaagatgtagtttccctggtaatatctattcttctccacagGCTCAGTGTATTAGCAGACTACTATAAGATGGCCCTGGATTGCTTCTTTGCTGTGTGGTTTGTGGTTGGTAATGTATGGATTTTTGGAGGACACTCCTCT

Basic information

species Vitis vinifera
transcript Vv11s0016g04450.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0016g04450.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os02g54624.1 (Oryza sativa), 3'ss of exon 2
acatagtgtttgtaaaactgtgtttctatgcatgctttgtattagaatcttaattatgaaaagatgtagtttccctggtaatatctattcttctccacagGCTCAGTGTATTAGCAGACTACTATAAGATGGCCCTGGATTGCTTCTTTGCTGTGTGGTTTGTGGTTGGTAATGTATGGATTTTTGGAGGACACTCCTCT
|| | ||| | | || | | | | || | ||||| | ||| ||| | | | | || | | | | || |||| | | || | ||| ||| ||||||||| ||||||| |||||||||||||||||||| || || ||||| ||||| ||||| || | || |||
ctgaagcatctgtgtatgagcattgcaaggaacactattgtttagattgttatttacacatgttcacaatgttgctatttaaagacaaatgccttttcagGATTAATGCTCTTTTTGACCACTTCAAGATGGCCTTGGATTGTTTCTTTGCTGTGTGGTTTGTCGTAGGAAATGTGTGGATATTTGGCGGGCGTTCTTCT

upper sequence: Vv11s0016g04450.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os01g08340.1 (Oryza sativa), 3'ss of exon 3
---acatagtgtttgtaaaactgtgtttctatgcatgctttgtattagaatcttaattatgaaaagatgtagtttccctggtaatatctattcttctccacagGCTCAGTGTATTAGCAGACTACTATAAGATGGCCCTGGATTGCTTCTTTGCTGTGTGGTTTGTGGTTGGTAATGTATGGATTTTTGGAGGACACTCCTCT
| | || | | || | || | | | | || || ||| || | || || | | ||| || | | || | ||| || | ||| | | | || || |||| |||||||| |||||||||||||||||||| ||||| ||||| ||||| || || || | | |||
atactagaagattcaacatcatatgaaaccatctgagttctttcttctaactaacatt-tggattcattta--tgaggtaacaatgccttctgtgctttatagGGTCTACGCATTGGTTGCGTGCTTCAAATTGGCTCTGGATTGTTTCTTTGCTGTGTGGTTTGTTGTTGGGAATGTGTGGATATTCGGGGGCCGTACTTCT

upper sequence: Vv11s0016g04450.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os09g15430.4 (Oryza sativa), 3'ss of exon 2
-acatagtgtttgtaaaactgtgtttctatgcatgct-ttgtattagaatcttaattatgaaaagatgtagtttccctggtaatatctattcttctccacagGCTCAGTGTATTAGCAGACTACTATAAGATGGCCCTGGATTGCTTCTTTGCTGTGTGGTTTGTGGTTGGTAATGTATGGATTTTTGGAGGACACTCCTCT
| || |||| | || || || || | | ||| | | | || | ||| | | | | ||| | | |||||| || |||| || | | | |||| || | || || ||||||||||| |||||||| ||||| ||||| ||||||||||| || ||| | ||
taagtaa-atttgaagaaatgcgtgatgcgagatcttatagtacttagttttgtgcta-aatttgatatggatgtattaactgaggtgattatacattacagGCCTAGCATATTGGCTTATCATTTCAAGACAGCTGTAGACTGTTTCTTTGCTGTATGGTTTGTTGTTGGCAATGTGTGGATTTTTGGTGGGCACAGCACT

upper sequence: Vv11s0016g04450.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os05g08610.4 (Oryza sativa), 3'ss of exon 3
---acatagtgtttgtaaaactgtgtttctatgcatgctttgtattagaatcttaattatgaaaagatgtagtttccctggtaatatct-attcttctccacagGCTCAGTGTATTAGCAGACTACTATAAGATGGCCCTGGATTGCTTCTTTGCTGTGTGGTTTGTGGTTGGTAATGTATGGATTTTTGGAGGACACTCCTCT
| | || || | | || | | | ||| ||| | ||| | | | | ||| | || ||| | || ||| || | || || || ||| || ||||| ||||| || ||||||||||||||||| || || || ||||||||| | ||||| ||||| || |||
aataaactacgtatggtcttccagagatttaagtttcccatgttttattaacttttcctttag----tccaagttctgagctacagtcttaccatttgttttagGTTCCAAGCTTTTGCTGATCACTTCAAAATGGCTCTGGACTGTTTCTTTGCTGTGTGGTTCGTTGTGGGAAATGTATGGGTATTTGGTGGACATTCTTCT

upper sequence: Vv11s0016g04450.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G089466_T01 (Zea mays), 3'ss of exon 2
----------------------------------acatagtgtttgtaa-aactgtgttt--ctat-gcatgctttgtattagaatcttaattatgaaaagatgtagtttccctggtaatatctattcttctccacagGCTCAGTGTATTAGCAGACTACTATAAGATGGCCCTGGATTGCTTCTTTGCTGTGTGGTTTGTGGTTGGTAATGTATGGATTTTTGGAGGACACTCCTCT
|| ||| || | | ||||| || | | || ||||| | || | | || | | | || ||| | | | || |||| ||| || | ||| ||| ||||||||||||||||| |||||||| || |||||||| ||||| || || ||||| ||||| || | || |||
gtactcatgccttctttttttccttaaaaaaatggatcggtatttacaatgaatatgtttgactgtcacttgttttgtttatttatggtgctgcaaaatggctatgcattaaagatgaatgccctgtgctatctgcagGATCAATGCGCTGTTTGACCACTTCAAGATGGCCCTGGATTGTTTCTTTGCCGTCTGGTTTGTTGTTGGAAACGTGTGGATATTTGGTGGCCGTTCTTCT

upper sequence: Vv11s0016g04450.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G116952_T03 (Zea mays), 3'ss of exon 2
acatagtgtttgtaaaactgtgtttctatgcatgctttgtattagaatcttaattatgaaaagatgtagtttccctggtaatatctattcttctccacagGCTCAGTGTATTAGCAGACTACTATAAGATGGCCCTGGATTGCTTCTTTGCTGTGTGGTTTGTGGTTGGTAATGTATGGATTTTTGGAGGACACTCCTCT-----------------------------------
||||||| ||||| | || | ||| |||| | | || || ||||||||||| |||||||| ||||| ||||| ||||||||||| || | | |
------------------------------------------------------------------------------------------------acaggcttagtgtgctggcttatcacttcaagacaggtgttgactgtttctttgctgtatggtttgttgttggcaatgtgtggatttttggtgggcgcagTATTTCATCAGATGCTCAGGACGCTCCCAATATGTACAG

upper sequence: Vv11s0016g04450.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G116952_T07 (Zea mays), 3'ss of exon 2
acatagtgtttgtaaaactgtgtttctatgcatgctttgt-attaga---atcttaattatgaaaaga----tgtagtttccctggtaatatctattcttctccacagGCTCAGTGTATTAGCAGACTACTATAAGATGGCCCTGGATTGCTTCTTTGCTGTGTGGTTTGTGGTTGGTAATGTATGGATTTTTGGAGGACACTCCTCT
||| | || || || || | || ||||| |||| | ||||| || ||| || | | | | ||| ||||||| ||||| | || | ||| |||| | | || || ||||||||||| |||||||| ||||| ||||| ||||||||||| || | | |
-------tcttgaagaattgagtggtctgatatattgagtcattagttttatctggaaactgaaatgaacattgtggtctgaactctgaagtg-attacatattacagGCTTAGTGTGCTGGCTTATCACTTCAAGACAGGTGTTGACTGTTTCTTTGCTGTATGGTTTGTTGTTGGCAATGTGTGGATTTTTGGTGGGCGCAGTATT

upper sequence: Vv11s0016g04450.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: EFJ36853 (Selaginella moellendorffii), 3'ss of exon 1
acatagtgtttgtaaaactgtgtttctatgcatgctttgtattagaatcttaattatgaaaagatgtagtttccctggtaatatctattcttctccacagGCTCAGTGTATTAGCAGACTACTATAAGATGGCCCTGGATTGCTTCTTTGCTGTGTGGTTTGTGGTTGGTAATGTATGGATTTTTGGAGGACACTCCTCT---------
|||| ||||| | || |||| |||| | || | | | | | |||||||| || || | | | | || | | ||||| || ||||||||||||| || |||||||| || ||||| || || ||||| ||||| |||||||||||
-------------------------gtatg-gtgcttccttttgctgtcttttttatacttttctctattgttcttcgactaatctattcatc-----agtgttggaagGCTGGTGGAGAAGTTCAAGATTGCGTTGGATTGCTTCTTCGCGGTGTGGTTCGTCGTTGGGAACGTGTGGATATTTGGCGGACACTCCTCGTCCCGCGAA

upper sequence: Vv11s0016g04450.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: EFJ27808 (Selaginella moellendorffii), 3'ss of exon 1
--------------acatagtgtttgtaaaactgtgtttctatgcatg---ctttgtattagaatcttaattatgaaaagatgtagtttccctggtaatatctattcttctccacagGCTCAGTGTATTAGCAGACTACTATAAGATGGCCCTGGATTGCTTCTTTGCTGTGTGGTTTGTGGTTGGTAATGTATGGATTTTTGGAGGACACTCCTCT
|| | | | | | ||| | ||| ||| | || |||| |||| | || | | | | | |||||||| || || | | | | || | | ||||| || ||||||||||||| || |||||||| || ||||| || || ||||| ||||| |||||||||||
gtcgcgaggaagggacgtggattccgcgag-tgacaattcggggtatggtgcttccttttgctttcttttttatatttttctctattgttcttcgactaatctattcatc-----agTGTTGGAAGGCTGGTGGAGAAGTTCAAGATTGCGTTGGATTGCTTCTTCGCGGTGTGGTTCGTCGTTGGGAACGTGTGGATATTTGGCGGACACTCCTCG

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|34545153|gb|CF513385.1|CF513385
EST:     GGAATGGTCATACTATGGGTGCTTCAAATGCTAG                         GCTCAGTATATTAGCAGACTACTATAAGATGGCCCTGGATTGCTTCTTTGC
genomic: GGAATGGTCATACTATGGGTGCTTCAAATGCTAGgtaaccactt ... ttctccacagGCTCAGTGTATTAGCAGACTACTATAAGATGGCCCTGGATTGCTTCTTTGC
EST: gi|110364081|gb|EC927724.1|EC927724
EST:     ACAAACACTTGGAATGGTCATACTATGGGTGCTTCAAATGCTAG                         GCTCAGTATATTAGCAGACTACTATAAGATGGCCCTGGATTGCTTCTTTGC
genomic: ACAAACACTTGGAATGGTCATACTATGGGTGCTTCAAATGCTAGgtaaccactt ... ttctccacagGCTCAGTGTATTAGCAGACTACTATAAGATGGCCCTGGATTGCTTCTTTGC
EST: gi|156737947|gb|EV242068.1|EV242068
EST:     GCGTCTACAAACACTTGGAATGGTCATACTATGGGTGCTTCAAATGCTAG                         GCTCAGTGTATTAGCAGACTACTATAAGATGGCCCTGGATTGCTTCTTTGC
genomic: GCGTCTACAAACACTTGGAATGGTCATACTATGGGTGCTTCAAATGCTAGgtaaccactt ... ttctccacagGCTCAGTGTATTAGCAGACTACTATAAGATGGCCCTGGATTGCTTCTTTGC
EST: gi|34546148|gb|CF514380.1|CF514380
EST:     GCGTCTACAAACACTTGGAATGGTCATACTATGGGTGCTTCAAATGCTAG                         GCTCAGTATATTAGCAGACTACTATAAGATGGCCCTGGATTGCTTCTTTGC
genomic: GCGTCTACAAACACTTGGAATGGTCATACTATGGGTGCTTCAAATGCTAGgtaaccactt ... ttctccacagGCTCAGTGTATTAGCAGACTACTATAAGATGGCCCTGGATTGCTTCTTTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatcttaattatgaaaagatgtagtttccctggtaatatctattcttctccacagGCTCAGTGTATTAGCAGACTACTATAAGATGGCCCTGGATTGCTTCTTTGCTGTGTGGTTTGTGGTTGGTAATGTATGGATTTTTGGAGGACACTCCTCT
  tcttaat  putative branch site (score: 3)
 tatctattcttctcc  putative PPT
 taattatgaaaagat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acatagtgtttgtaaaactgtgtttctatgcatgctttgtattagaatcttaattatgaaaagatgtagtttccctggtaatatctattcttctccacagGCTCAGTGTATTAGCAGACTACTATAAGATGGCCCTGGATTGCTTCTTTGCTGTGTGGTTTGTGGTTGGTAATGTATGGATTTTTGGAGGACACTCCTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - -gtaaaac
- - - - - - - - - - - - - - -gcatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaaaga