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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atatcctattcgctaatttggtgattttccctagaactttttcttgtgccttgtgtttctcgtgtatcaatcaatcctccggttcttccggttcttgcagGCAGCAAACTATCTAGATATCAAGAGCCTGTTGGATTTGACCTGCCAAACAGTTGCTGACATGATCAAGGGAAAGACTCCGGAGGAAATTCGCAAGACAT

Basic information

species Vitis vinifera
transcript Vv03s0038g02500.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv03s0038g02500.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os09g36830.1 (Oryza sativa), 3'ss of exon 1
atatcctattcgctaatttggtgattttccctagaactttttcttgtgccttgtgtttctcgtgtatcaa-tcaatc---ctccggttcttccggttcttgcagGCAGCAAACTATCTAGATATCAAGAGCCTGTTGGATTTGACCTGCCAAACAGTTGCTGACATGATCAAGGGAAAGACTCCGGAGGAAATTCGCAAGACAT
   | ||    | |  | |  || || |   |  | |  | | |  ||  || | |   || ||||  || || ||     ||  || | |     | || ||||| |||||||| ||  | |||||| | ||| ||||| |||||||||| || || ||||||||||||||||| ||||| || ||||| || |||||||| |
---tgctggatgattgtctcatgcttctgt-tgtatccatgtatattgttttttatcattcatgtacaaagtcgattagattcatgtgcatgtttgtgtttcagGCTGCAAACTACCTCAACATCAAGGGACTGCTGGATCTGACCTGCCAGACCGTGGCTGACATGATCAAGGGGAAGACACCAGAGGAGATCCGCAAGACCT

upper sequence: Vv03s0038g02500.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os11g26910.1 (Oryza sativa), 3'ss of exon 1
atatcctattcgctaatttggtgattttccctagaactttttcttgtgccttgtgtttctcgtgtatcaatcaatcctccggttcttc-cggttcttgcagGCAGCAAACTATCTAGATATCAAGAGCCTGTTGGATTTGACCTGCCAAACAGTTGCTGACATGATCAAGGGAAAGACTCCGGAGGAAATTCGCAAGACAT
 |   ||||    |  ||| |||  |     | || || |   ||   | | ||| ||   |  | | |  | ||  |    |  ||| |   ||   ||||| || ||||| ||  | |||||| |  || ||||  | || ||||| || |||||||||||||||||||| |||||||| ||||| || |||||||| |
-tgaactatgtattccttttgtggctgaatgttgatctgtgctttagccatagtgattactgcttcttataccatgtttatttgattctcaaatcccacagGCCGCGAACTACCTCAACATCAAGGGGTTGCTGGACCTTACTTGCCAGACTGTTGCTGACATGATCAAGGGGAAGACTCCTGAGGAGATCCGCAAGACCT

upper sequence: Vv03s0038g02500.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G101446_T01 (Zea mays), 3'ss of exon 1
atatcctattcgctaatttggtgattttccctagaactttttcttgtgccttgtgtttctcgtgtatcaatcaatcct---ccggttcttccg-gttcttgcagGCAGCAAACTATCTAGATATCAAGAGCCTGTTGGATTTGACCTGCCAAACAGTTGCTGACATGATCAAGGGAAAGACTCCGGAGGAAATTCGCAAGACAT
  |  || ||   |  |||| |  || |  |   || | | |  |||   ||||  || | || |    |    | ||    || |||| ||    | ||  |||| |||||||||||  | |||||| | ||| | ||  ||||||| || || |||||||||||||||||||| ||||| || || || ||||||||||| |
-cacactgttt--ttgtttgatttttgtatc-gtaattatatactgtaaattgtaattattgtttgagcactgcttctgattcgtttctcccctaattttatagGCTGCAAACTATCTGAACATCAAGGGTCTGCTCGACCTGACCTGTCAGACTGTTGCTGACATGATCAAGGGCAAGACACCAGAAGAGATTCGCAAGACCT

upper sequence: Vv03s0038g02500.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: EFJ22022 (Selaginella moellendorffii), 3'ss of exon 1
-----atatcct-attcgctaatttggtgattttccctagaactttt----tcttgtgccttgtgtttctcgtgtatcaatcaatcc------tccggttcttccggttcttgcagGCAGCAAACTATCTAGATATCAAGAGCCTGTTGGATTTGACCTGCCAAACAGTTGCTGACATGATCAAGGGAAAGACTCCGGAGGAAATTCGCAAGACAT
     || || |  |||| |   ||      |||  ||    |||||    | ||| | |||| | || |||  |  ||||| ||        || |||| | |  ||| || ||||| || ||||||||  | |||  || | || ||||| |||| |||||||| || || |||||||||||||| ||||| |||||||| || |||||||| |
gtaggatttcttcgttcgatttcttcccccctttttctctcgcttttctcgttttgggtcttgagctt-tcgactgacaatcgatttgggtgatctggttttgc--gttgttccagGCCGCGAACTATCTCAACATCCGGAACTTGCTGGATCTGACGTGCCAAACCGTGGCGGACATGATCAAGGGCAAGACCCCGGAGGAGATCCGCAAGACTT

upper sequence: Vv03s0038g02500.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: EFJ18284 (Selaginella moellendorffii), 3'ss of exon 1
atatcctattcgctaatttggtgattttccctagaactttttcttgtgccttgtgtt---tctcgtgtatcaatcaatcctccggttcttccggttc-ttgcagGCAGCAAACTATCTAGATATCAAGAGCCTGTTGGATTTGACCTGCCAAACAGTTGCTGACATGATCAAGGGAAAGACTCCGGAGGAAATTCGCAAGACAT
   |   |||   |  || | |   || |||      | | ||   |  || || ||   ||| | |  |    |   |   || ||     | ||  || ||||| || ||||||||  | |||  || | || ||||| |||| |||||||| || || |||||||||||||| ||||| |||||||| || |||||||| |
--gtaggatttcttcgttcgatttcttcccccctttttctctcgcttttctcgttttgggtcttgagctttcgactgacaatcgatttgggtgatttgttccagGCCGCGAACTATCTCAACATCCGGAACTTGCTGGATCTGACGTGCCAAACCGTGGCGGACATGATCAAGGGCAAGACCCCGGAGGAGATCCGCAAGACTT

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|161707912|gb|FC056958.1|FC056958
EST:     ATGCTGATTTCGTGAAATTCGATCAGGCCACCCTCTTTGACCTCATCTTG                         GCAGCAAACTATCTAGATATCAAGAGCCTGTTGGATTTGACCTGCCAAACA
genomic: ATGCTGATTTCGTGAAAGTCGATCAGGCCACCCTCTTTGACCTCATCTTGgtgagacttc ... gttcttgcagGCAGCAAACTATCTAGATATCAAGAGCCTGTTGGATTTGACCTGCCAAACA
EST: gi|110420231|gb|EC986496.1|EC986496
EST:     ATGCTGATTTCGTGAAAGTAGATCAGGCCACCCTCTTTGACCTCATCTTG                         GCAGCAAACTATCTAGATATCAAGAGCCTGTTGGATTTGACCTGCCAAACA
genomic: ATGCTGATTTCGTGAAAGTCGATCAGGCCACCCTCTTTGACCTCATCTTGgtgagacttc ... gttcttgcagGCAGCAAACTATCTAGATATCAAGAGCCTGTTGGATTTGACCTGCCAAACA
EST: gi|110691759|gb|EE070229.1|EE070229
EST:     ATGCTGATTTCGTGAAAGTCGATCAGGCCACCCTCTTTGACCTCATCTTG                         GCAGCAAACTATCTAGATATCAAGAGCCTGTTGGATTTGACCTGCCAAACA
genomic: ATGCTGATTTCGTGAAAGTCGATCAGGCCACCCTCTTTGACCTCATCTTGgtgagacttc ... gttcttgcagGCAGCAAACTATCTAGATATCAAGAGCCTGTTGGATTTGACCTGCCAAACA
EST: gi|110692938|gb|EE068734.1|EE068734
EST:     ATGCTGATTTCGTGAAAGTCGATCAGGCCACCCTCTTTGACCTCATCTTG                         GCAGCAAACTATCTAGATATCAAGAGCCTGTTGGATTTGACCTGCCAAACA
genomic: ATGCTGATTTCGTGAAAGTCGATCAGGCCACCCTCTTTGACCTCATCTTGgtgagacttc ... gttcttgcagGCAGCAAACTATCTAGATATCAAGAGCCTGTTGGATTTGACCTGCCAAACA
EST: gi|30127342|gb|CB912681.1|CB912681
EST:     ATGCTGATTTCGTGAAAGTCGATCAGGCCACACTCTTTGACCTCATCTTG                         GCAGCAAACTATCTAGATATCAAGAGCCTGTTGGATTTGACCTGCCAAACA
genomic: ATGCTGATTTCGTGAAAGTCGATCAGGCCACCCTCTTTGACCTCATCTTGgtgagacttc ... gttcttgcagGCAGCAAACTATCTAGATATCAAGAGCCTGTTGGATTTGACCTGCCAAACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgccttgtgtttctcgtgtatcaatcaatcctccggttcttccggttcttgcagGCAGCAAACTATCTAGATATCAAGAGCCTGTTGGATTTGACCTGCCAAACAGTTGCTGACATGATCAAGGGAAAGACTCCGGAGGAAATTCGCAAGACAT
                                     ttcttccggttctt  CT-rich tract
                   tatcaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atatcctattcgctaatttggtgattttccctagaactttttcttgtgccttgtgtttctcgtgtatcaatcaatcctccggttcttccggttcttgcagGCAGCAAACTATCTAGATATCAAGAGCCTGTTGGATTTGACCTGCCAAACAGTTGCTGACATGATCAAGGGAAAGACTCCGGAGGAAATTCGCAAGACAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - tggtgat
- - - - - - - - - - - - - - - - - - - - - cttgtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caatcaa