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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gataatgaaataaaaaaatatttctttattttctatttttgatatgattttgtgaatttagattagggtgatgtctgataatgttgctgaatgatcgcagGTATGTATTTGGAGTGACACACATTCCTCGCCTGGAAGACTGGCCTGTCATGCCAGTGGAGCACATTGGTTTTAGGCTCATG

Basic information

species Vitis vinifera
transcript Vv00s0225g00090.t01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s0225g00090.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: LOC_Os04g40040.1 (Oryza sativa), 3'ss of exon 11
gataatgaaataaaaaaatatttctttattttctatttttgatatgattttgtgaatttagattagggtgatgtctgataatgttgctgaatgatcgcagGTATGTATTTGGAGTGACACACATTCCTCGCCTGGAAGACTGGCCTGTCATGCCAGTGGAGCACATTGGTTTTAGGCTCATG
               | |  |     ||   |  || | || ||   || |  |  |   || | ||   ||   || |||   | |         |||||||||| |||||  | || || || ||  | ||||| ||||||||||||||||||||||| | ||| || || | |||||||
-------------gtatacttgctactacgatgcatctgtg-taactttcttcggttcacgactgggaatattgttgttaactatacactgcatctgcagGTATGTGTTTGGGCTCACCCATATCCCAAGGCTGGAGGACTGGCCTGTCATGCCAGTGGAACGCATCGGCTTCATGCTCATG

upper sequence: Vv00s0225g00090.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA18G20800.1 (Glycine max), 3'ss of exon 10
gataatgaaataaaaaaatatttctttattttctatttttga-tatgattttgtgaatttagattagggtgatgtctgataatgttgctgaatgatcgcagGTATGTATTTGGAGTGACACACATTCCTCGCCTGGAAGACTGGCCTGTCATGCCAGTGGAGCACATTGGTTTTAGGCTCATG
  |   || || ||  |    |   || | ||   |   ||| |   |   ||   |||||  ||  |   ||||||  | || | |  |||   | ||||||| ||||||||||||||||||||||||||  |||||||||||||||| ||||| ||||| | ||||||||| | ||| |||
-gtggcgacatcaatcaggtgtcacttgtattacgtccatgaatcctaacatgcttatttattttttgcatatgtctatttatttggtggaaatgttgcagGTACGTATTTGGAGTGACACACATTCCTCGATTGGAAGACTGGCCTGTTATGCCCGTGGAACGCATTGGTTTCATGCTTATG

upper sequence: Vv00s0225g00090.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA08G38990.1 (Glycine max), 3'ss of exon 10
gataatgaaataaaaaaatatt-tctttattttctatttttgatatgattttgtgaatttagattagggtgatgtctgataatgt-tgctgaatgatcgcagGTATGTATTTGGAGTGACACACATTCCTCGCCTGGAAGACTGGCCTGTCATGCCAGTGGAGCACATTGGTTTTAGGCTCATG
  ||   ||      |  |    ||  |   |  || || |  | | |   |  |   | |  ||  ||| || | |  |      ||  |||   | ||||||| |||||||||||||||||||||||| |  |||||||||||||||| ||||| ||||| | ||||||||| | ||| |||
--tagctaaggcctgaggtgccatcaatgactgataattgttgttttagactcagttctgatgttgtggttatttatttttgcacatgtcgaaatgttgcagGTACGTATTTGGAGTGACACACATTCCTAGATTGGAAGACTGGCCTGTTATGCCCGTGGAACGCATTGGTTTCATGCTTATG

upper sequence: Vv00s0225g00090.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA02G04360.1 (Glycine max), 3'ss of exon 10
-------gataatgaaataaaaaaatatttctttattttctatttttgatatgattttgtgaatttagattagggtgatgtctgataatgttgctgaatgatcgcagGTATGTATTTGGAGTGACACACATTCCTCGCCTGGAAGACTGGCCTGTCATGCCAGTGGAGCACATTGGTTTTAGGCTCATG
        |  |    ||  |   ||| || |    |||    ||||| | ||  ||| || |||     ||   || | |||||||    ||  | |  ||  |||||| || |||||  | ||||||||||| ||  ||||||||||||| || ||||||||||| | |||||| |||| ||| |||
cacactttaagacatcattgactgataattgtactctttgggattttgttgtg--tttatgcattctttataca-tgttatctgata----tgaaggactatttcagGTACGTGTTTGGTATAACACACATTCCCCGATTGGAAGACTGGCCAGTTATGCCAGTGGAACGCATTGGCTTTATGCTTATG

upper sequence: Vv00s0225g00090.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: PP1S178_54V6.1 (Physcomitrella patens), 3'ss of exon 12
gataatgaaataaaaaaatatttctttattttctatttttgatatgattttgtgaatttagattaggg------tgatgtctgataatgttgctgaatgatcgcagGTATGTATTTGGAGTGACACACATTCCTCGCCTGGAAGACTGGCCTGTCATGCCAGTGGAGCACATTGGTTTTAGGCTCATG
      |  ||    | |  || | || |  |||   | || |  | | |    |  || | | | |       ||  || || | |   |       ||   |||||||||||||||||| || ||||||||| | || ||||||||||| || ||||| |||||||||||||| || ||  | |||
------gggattgttagagtttgcgttgtagtcttaatatggtgaggtatctcaatgtttgttcatgcaattgctgtggtatgctcacactttcctcggagtccagGTATGTATTTGGAGTTACTCACATTCCTAGACTTGAAGACTGGCCAGTAATGCCTGTGGAGCACATTGGATTCAGTTTGATG

upper sequence: Vv00s0225g00090.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: PP1S9_129V6.2 (Physcomitrella patens), 3'ss of exon 5
gataatgaaataaaaaaatatttctttattttctatttttgatatgattttgtgaattt---agattagggtgatgtctgataatgttgctgaatgatcgcagGTATGTATTTGGAGTGACACACATTCCTCGCCTGGAAGACTGGCCTGTCATGCCAGTGGAGCACATTGGTTTTAGGCTCATG
     | |  |  ||   || || |   |        | | |||||  | ||||||  |   | | || | | |  ||   |        |   |||  ||||||||||||||||||| || ||||| ||| | |||||||| ||||| || ||||| |||||||||||||| || ||  |  ||
--cctttacttgtaactttacttgtgggtagggagcctat-atatgcgtctgtgaaactgccataatatgcttacatcctttctgcaatttatttgagtgcagGTATGTATTTGGAGTCACTCACATACCTAGACTGGAAGATTGGCCAGTTATGCCTGTGGAGCACATTGGATTCAGTTTGGTG

upper sequence: Vv00s0225g00090.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: PP1S26_107V6.1 (Physcomitrella patens), 3'ss of exon 9
-----------------------------------------------------------gataatgaaataaaaaaatatttctttat--tttc---tatttttgatatgattttgtgaatttagattag---ggtgatgtctgataatgttgctgaatgatcgcagGTATGTATTTGGAGTGACACACATTCCTCGCCTGGAAGACTGGCCTGTCATGCCAGTGGAGCACATTGGTTTTAGGCTCATG
                                                            | |||    ||   |||| | |    |   ||||   |  || |  ||||  |  || |||   | ||      |  |  ||| |       | |  ||| | |||||||||| ||||| ||||| ||| | ||||| || ||||| |||||||||||||| ||||||||| |||| || |  ||  ||
gtaatcccctgacttgacatttaatttgtcatattgacacccttgcaaagcagggatgttacaatatcgtacgtaaatgtcttcagaggatttcgagtgattcttgtatgtctacgtaaatcatgctttatttagctagatctaagggctcggtt--atgcttgcagGTATGTCTTTGGTGTGACGCACGTCCCTCGTCTTGAAGATTGGCCTGTCATGCCTGTGGAGCACGTTGGCTTCAAACTTCTG

upper sequence: Vv00s0225g00090.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: EFJ13052 (Selaginella moellendorffii), 3'ss of exon 9
gataatgaaataaaaaaatatttctttattttctatttttgatatgattttgtgaatttagattagggtgatgtctgataatgtt-gctgaatg-atcgcagGTATGTATTTGGAGTGACACACATTCCTCGCCTGGAAGACTGGCCTGTCATGCCAGTGGAGCACATTGGTTTTAGGCTCATG
                              |  || | | |    ||| |        |   ||   |  |  |||  || |  | | |  ||| | |||||||| |||||||||||||||||||| ||| | || || || ||||| || ||||||||||||| ||| || || |  |||| |
-----------------------------gtaatactctaggatcgatctctccttcctctcttctcgcaaaatctcctagttctcgatcgatgcaacgcagGTACGTATTTGGAGTGACACACATACCTAGGCTCGAGGATTGGCCCGTGATGCCAGTGGAGCGCATCGGATTCACACTCACG

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|110429682|gb|EC996183.1|EC996183
EST:     ACTTGGGTTAACCAGAATAGATCGTTGGAAGAAACAGACATAGTTCTTTG                         GTATGTATTTGGAGTGACACACATTCCTCGCCTGGAAGACTGGCCTGTCAT
genomic: ACTTGGGTTAACCAGAATAGATCGTTGGAAGAAACAGACATAGTTCTTTGgttagttttt ... atgatcgcagGTATGTATTTGGAGTGACACACATTCCTCGCCTGGAAGACTGGCCTGTCAT
EST: gi|83275167|gb|DV939263.1|DV939263
EST:     ACTTGGGTTAACCAGAATAGATCGTTGGAAGAAACAGACATAGTTCTTTG                         GTATGTATTTGGAGTGACACACATTCCTCGCCTGGAAGACTGGCCTGTCAT
genomic: ACTTGGGTTAACCAGAATAGATCGTTGGAAGAAACAGACATAGTTCTTTGgttagttttt ... atgatcgcagGTATGTATTTGGAGTGACACACATTCCTCGCCTGGAAGACTGGCCTGTCAT
EST: gi|71874908|gb|DT023963.1|DT023963
EST:     ACTTGGGTTAACCAGAATAGATCGTTGGAAGAAACAGACATAGTTCTTTG                         GTATGTATTTGGAGTGACACACATTCCTCGCCTGGAAGACTGGCCTGTCAT
genomic: ACTTGGGTTAACCAGAATAGATCGTTGGAAGAAACAGACATAGTTCTTTGgttagttttt ... atgatcgcagGTATGTATTTGGAGTGACACACATTCCTCGCCTGGAAGACTGGCCTGTCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gattttgtgaatttagattagggtgatgtctgataatgttgctgaatgatcgcagGTATGTATTTGGAGTGACACACATTCCTCGCCTGGAAGACTGGCCTGTCATGCCAGTGGAGCACATTGGTTTTAGGCTCATG
                           gtctgat  putative branch site (score: 4)
         aatttagatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gataatgaaataaaaaaatatttctttattttctatttttgatatgattttgtgaatttagattagggtgatgtctgataatgttgctgaatgatcgcagGTATGTATTTGGAGTGACACACATTCCTCGCCTGGAAGACTGGCCTGTCATGCCAGTGGAGCACATTGGTTTTAGGCTCATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- -aatgaaa
- - - - - -aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtctga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttgct