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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttccatagtctcactgtacctattgattgatgactctgtgattagtgattactgattacagttcccaataattattttctatttttgaaaaacaaaaacagtttaccttcagcttacaaaatcagtgtttggttacacagGGCCTTGGAATTACCGTGTTTGGAATGGCCTACATGTTTGTCCACGATGGTCTCGTCCACAGGAGATTTCCAGTGGGGCCCATTGCGAACGTGCCCTATT

Basic information

species Vitis vinifera
transcript Vv16s0050g01090.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0050g01090.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os10g38940.1 (Oryza sativa), 3'ss of exon 2
gtaagttccatagtctcactgtacctattgattgatgactctgtgattagtgattactgattacagttcccaataattattttctatttttgaaaaacaaaaacagtttaccttcagcttacaaaatcagtgtttggttacacagGGCCTTGGAATTACCGTGTTTGGAATGGCCTACATGTTTGTCCACGATGGTCTCGTCCACAGGAGATTTCCAGTGGGGCCCATTGCGAACGTGCCCTATT
                                   | ||   ||| |  | |        |  | |||   |     | || | |||  |   |        ||   | || |   | |  |     |   |    |    |||||| ||||| |||||  |||| || ||||| |||||||| |||||||| || || |||||| || | || || ||||||||||| | |||||||||||| |
----------------------------------gtcacgtcgtggtcgggggc-----gtatccgttttgag--gctcttctttatcgtctgatgg--gtgacgtgtcacgt--ggttggcgctgacgtggccgcgcgcaacagGGGCTTGGGATTACGCTGTTCGGGATGGCGTACATGTTCGTCCACGACGGCCTGGTCCACCGGCGCTTCCCCGTGGGGCCCATCGAGAACGTGCCCTACT

upper sequence: Vv16s0050g01090.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G164318_T01 (Zea mays), 3'ss of exon 3
gtaagttccatagtctcactgtacctattgattg-atgactctgtgattagt--gattactgattacagttcccaataattattttctatttttga-aaaacaaaaacagtttaccttcagcttacaaaatcagtgt-ttggttacacagGGCCTTGGAATTACCGTGTTTGGAATGGCCTACATGTTTGTCCACGATGGTCTCGTCCACAGGAGATTTCCAGTGGGGCCCATTGCGAACGTGCCCTATT
||||| |    |    || | |  |  |   |||  || ||   |  || ||  | |  |||    ||| |         ||       |   ||     |   |   |    ||  | | || ||       |||| ||  |  |||||||||| || |||||  |||| || |||||||||||||| |||||||| || || |||||| |  | ||||| || || ||||| || ||||||||||| |
gtaagctagccacgtacagtatctcggtgtgttgtgtgtctggttagttggttggctggctggacccagctgttgcctggtaggcagggtggctggcgtcagccacgtatccgactgtgatctcaccctccacgtgtcttcctcccacagGGCCTCGGGATTACGCTGTTCGGCATGGCCTACATGTTCGTCCACGACGGCCTGGTCCACCGCCGCTTTCCGGTCGGCCCCATCGCCAACGTGCCCTACT

upper sequence: Vv16s0050g01090.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G152135_T06 (Zea mays), 3'ss of exon 3
----gtaagttccatagtctc--actgtacctattgattgatgactctgtgattagt--gattactgattacagttcccaataattattttctatttttgaaaaacaaaaacagtttaccttcagcttacaaaatcagtgt-ttggttacacagGGCCTTGGAATTACCGTGTTTGGAATGGCCTACATGTTTGTCCACGATGGTCTCGTCCACAGGAGATTTCCAGTGGGGCCCATTGCGAACGTGCCCTATT
    |  || |   ||| | |  ||||| |||  | | |  |   |   || || ||  ||| ||  |   |  |   |  |  |   |  ||   | | |   ||      |    ||  | | || ||       |||| ||  |  |||||||||| || |||||  |||| || |||||||||||||| |||||||| || || |||||| |  | ||||| || || ||||| ||  |||||||||| |
gtaagctagctagctagccacggactgtgcctggttagtt-tagttagttggttggtcggatgacccacctctctcagcggtggtgcctgcctgcctgtcagccacggggg-atccgactgtgatctcaccctccacgtgtcttcatgtcacagGGCCTGGGGATTACGCTGTTCGGCATGGCCTACATGTTCGTCCACGACGGCCTGGTCCACCGCCGCTTTCCGGTCGGCCCCATCGCCGACGTGCCCTACT

upper sequence: Vv16s0050g01090.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA20G30230.1 (Glycine max), 3'ss of exon 4
gtaagttccatagtctcactgtacctattgattgatgactctgtgattagtgattactgattacagttcccaataattattttctatttttgaaaaacaaaaacagttta--ccttcagcttacaaaatcagtgtt-tggttacacagGGCCTTGGAATTACCGTGTTTGGAATGGCCTACATGTTTGTCCACGATGGTCTCGTCCACAGGAGATTTCCAGTGGGGCCCATTGCGAACGTGCCCTATT
            |  ||| |||| || |||||     | | | | |||| |   |  | ||||   |  ||| |||||| ||    |  ||  |    || | |     |   ||     | |    |||    |  |  ||   |||||||||||||| || |||||||| ||||||||||||||||||||||||||  | || || | |||||| || ||||| |||||||| ||||||||||| |
----------gtgagtcagtgtatct-ttgataatctaatttttaattaatccct--taattaggat--ccattaattaattgtagtgatttgacggtaataccctccaaaaactgtgaataatggcatcctcataatctttgagcagGGCCTTGGAATCACGGTGTTTGGGATGGCCTACATGTTTGTCCACGATGGATTGGTTCATAAGAGATTCCCTGTGGGTCCCATTGCCAACGTGCCCTACT

upper sequence: Vv16s0050g01090.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA20G30230.2 (Glycine max), 3'ss of exon 4
gtaagttccatagtctcactgtacctattgattgatgactctgtgattagtgattactgattacagttcccaataattattttctatttttgaaaaacaaaaacagtttac--cttcagcttacaaaatcagtgtt-tggttacacagGGCCTTGGAATTACCGTGTTTGGAATGGCCTACATGTTTGTCCACGATGGTCTCGTCCACAGGAGATTTCCAGTGGGGCCCATTGCGAACGTGCCCTATT
               ||| |||| || |||||     | | | | |||| |   |  | ||||   |  ||| |||||| ||    |  ||  |    || | |     |   ||     | |    |||    |  |  ||   |||||||||||||| || |||||||| ||||||||||||||||||||||||||  | || || | |||||| || ||||| |||||||| ||||||||||| |
--------------gtcagtgtatct-ttgataatctaatttttaattaatccct--taattaggat--ccattaattaattgtagtgatttgacggtaataccctccaaaaactgtgaataatggcatcctcataatctttgagcagGGCCTTGGAATCACGGTGTTTGGGATGGCCTACATGTTTGTCCACGATGGATTGGTTCATAAGAGATTCCCTGTGGGTCCCATTGCCAACGTGCCCTACT

upper sequence: Vv16s0050g01090.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA10G37560.2 (Glycine max), 3'ss of exon 4
gtaagttccatagtctcactgtacctattgattgatgactctgtgattagtgattactgattacagttcccaataattattttctatttttgaaaaacaaaaacagtttaccttcagcttacaaaatcagtgtttggttacacagGGCCTTGGAATTACCGTGTTTGGAATGGCCTACATGTTTGTCCACGATGGTCTCGTCCACAGGAGATTTCCAGTGGGGCCCATTGCGAACGTGCCCTATT
          ||   ||| |||| || | |     | | | | | ||   | | |     | || ||| |     |||    ||  ||  |  |||  || ||   |     ||   ||       |   | ||||      |||||||||||||| || || ||||| ||||||||||||||||||||||||||  | || || | |||||| || ||||| |||||||| ||||||||||| |
---------gtaag-tcagtgtatctttcgtaatctaattttttaatccctcaat-----taacggtttc-----attgggatccgttaattgaaattaagaatgatagtggtttgact------gttcatctttga----gcagGGCCTTGGAATCACGGTATTTGGGATGGCCTACATGTTTGTCCACGATGGATTAGTTCATAAGAGATTCCCTGTGGGTCCCATTGCCAACGTGCCCTACT

upper sequence: Vv16s0050g01090.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA16G29790.1 (Glycine max), 3'ss of exon 4
gtaagttccatagtctcactgtacctattgattgatgactctgtgattagtgattactgattacagttcccaataattattttctatttttgaaaaacaaaaacagtttaccttcagcttacaaaatcagtgtttggttacacagGGCCTTGGAATTACCGTGTTTGGAATGGCCTACATGTTTGTCCACGATGGTCTCGTCCACAGGAGATTTCCAGTGGGGCCCATTGCGAACGTGCCCTATT
                                  ||  |  |   | || | |||| |  ||| | ||       |||  | |  |||             |||| |||  ||       | | |  |  |      | | |||||| ||||||||||| || ||||| ||||||||||||||||| ||||||||  | || || | |||||| || ||||| |||||||| |||||||||||| 
--------------------------------aaataccaataaaaataataattattacttagactttaatgacattgatcttgatt------------gaacacttttactaagatagatagataccttcaactatga-acagGGTCTTGGAATTACGGTCTTTGGGATGGCCTACATGTTTGTACACGATGGATTGGTTCATAAGAGATTCCCGGTGGGCCCCATTGCAAACGTGCCCTATC

upper sequence: Vv16s0050g01090.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA09G24530.1 (Glycine max), 3'ss of exon 4
gtaagttccatagtctcactgtacctattgattgatgactctgtgattagtgattactgattacagttcccaataattattttctatttttgaaaaacaaaaacagtttaccttcagcttacaaaat-cagtgtttggttac--acagGGCCTTGGAATTACCGTGTTTGGAATGGCCTACATGTTTGTCCACGATGGTCTCGTCCACAGGAGATTTCCAGTGGGGCCCATTGCGAACGTGCCCTATT
                                              |||   | |||| || | |  |   ||| | || ||    ||||    | |   | |  | ||     |   |   || || |  | ||    ||   |||||| ||||||||||| || ||||| ||||||||||||||||| ||||||||  | || |||| |||||| || ||||| ||||| || |||||||||||| 
----------------------------------------------ttaccaaatactaataaaa--taataattactacttagacttttaatgacattgatattgattgaacacttttactaagatgccttcttcaactatgaacagGGTCTTGGAATTACTGTCTTTGGGATGGCCTACATGTTTGTACACGATGGATTGGTTCACAAGAGATTCCCGGTGGGCCCCATAGCCAACGTGCCCTATC

upper sequence: Vv16s0050g01090.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT4G25700.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaagttccatagtctcactgtacctattgattgatgactctgtgattagtgattactgattaca-gttcccaataattattttctatttttgaaaaacaaaaacagtttaccttcagcttacaaaatcagtgtttggttacacagGGCCTTGGAATTACCGTGTTTGGAATGGCCTACATGTTTGTCCACGATGGTCTCGTCCACAGGAGATTTCCAGTGGGGCCCATTGCGAACGTGCCCTATT
                                           |  |   | | || ||  |||| ||    |  ||| | ||| |    |  |  |||| |||     |     |    |   ||    ||  |||   | ||||||  | || || || ||||||||||| ||||||||||||||||||||||||||||| |||| | | || || || || ||||| ||  |||| || ||  
-------------------------------------------ttgtattttaatattggatacatgtgatgacaaatgactttgttggctgcattaacacaaatgacctggtggcttaattttaagctcgtccttg---aaacagGGGTTAGGCATAACGGTGTTTGGAATCGCCTACATGTTTGTCCACGATGGTCTCGTGCACAAGCGTTTCCCTGTAGGTCCCATCGCCGACGTCCCTTACC

upper sequence: Vv16s0050g01090.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT5G52570.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaagttccatagtctcactgtacctattgattgatgactctgtgattagtgattactgattacagttcccaataattattttctatttttgaaaaacaaaaacagtttaccttcagcttacaaaatcagtgtttggttacacagGGCCTTGGAATTACCGTGTTTGGAATGGCCTACATGTTTGTCCACGATGGTCTCGTCCACAGGAGATTTCCAGTGGGGCCCATTGCGAACGTGCCCTATT
                        | |   ||  | || |  |||  || | |  ||| || | |   |   |  | || | ||| ||| |               | |   ||  ||| ||    |   |||    | || ||||| || ||||| ||  ||||||||||||| |||||||| || |||||||| || || |||| |||||| || || || |||||||| ||||| || ||  
-----------------------tccaaacatgaaagattgggtg--tacttag-actaatgaaaccactatacgagtactatctgtttct---------------tgttttttgtgctgactggtt---tgtaatatcac-cagGGACTGGGAATAACGATGTTTGGAATGGCTTACATGTTCGTTCACGATGGACTTGTGCACAAGAGATTCCCTGTAGGTCCCATTGCCAACGTTCCTTACC

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|110362018|gb|EC925524.1|EC925524
EST:     CCTATGGCTTCTTCCACAAAGGCCTCGTCCCTGGTCTCTGTTTTGGTGCA                         GGCCTTGGAATTACCGTGTTTGGAATGGCCTACATGTTTGTCCACGATGGT
genomic: CCTATGGCTTCTTCCACAAAGGCCTCGTCCCTGGTCTATGTTTTGGTGCAgtaagttcca ... ggttacacagGGCCTTGGAATTACCGTGTTTGGAATGGCCTACATGTTTGTCCACGATGGT
EST: gi|110387779|gb|EC952475.1|EC952475
EST:     CCTATGGCTTCTTCCACAAAGGCCTCGTCCCTGGTCTCTGTTTTGGTGCA                         GGCCTTGGAATTACCGTGTTTGGAATGGCCTACATGTTTGTCCACGATGGT
genomic: CCTATGGCTTCTTCCACAAAGGCCTCGTCCCTGGTCTATGTTTTGGTGCAgtaagttcca ... ggttacacagGGCCTTGGAATTACCGTGTTTGGAATGGCCTACATGTTTGTCCACGATGGT
EST: gi|34549741|gb|CF517973.1|CF517973
EST:     CCTATGGCTTCTTCCACAAAGGCCTCGTCCCTGGTCTATGTTTTGGTGCA                         GGCCTTGGAATTACCGTGTTTGGAATGGCCTACATGTTTGTCCACGATGGT
genomic: CCTATGGCTTCTTCCACAAAGGCCTCGTCCCTGGTCTATGTTTTGGTGCAgtaagttcca ... ggttacacagGGCCTTGGAATTACCGTGTTTGGAATGGCCTACATGTTTGTCCACGATGGT
EST: gi|34544824|gb|CF513056.1|CF513056
EST:     CCTATGGCTTCTTCCACAAAGGCCTCGTCCCTGGTCTATGTTTTGGTGCA                         GGCCTTGGAATTACCGTGTTTGGAATGGCCTACATGTTTGTCCACGATGGT
genomic: CCTATGGCTTCTTCCACAAAGGCCTCGTCCCTGGTCTATGTTTTGGTGCAgtaagttcca ... ggttacacagGGCCTTGGAATTACCGTGTTTGGAATGGCCTACATGTTTGTCCACGATGGT
EST: gi|110422537|gb|EC988863.1|EC988863
EST:     CCTATGGCTTCTTCCACAAAGGCCTCGTCCCTGGTCTCTGTTTTGGTGCA                         GGCCTTGGAATTACCGTGTTTGGAATGGCCTACATGTTTGTCCACGATGGT
genomic: CCTATGGCTTCTTCCACAAAGGCCTCGTCCCTGGTCTATGTTTTGGTGCAgtaagttcca ... ggttacacagGGCCTTGGAATTACCGTGTTTGGAATGGCCTACATGTTTGTCCACGATGGT
EST: gi|110388927|gb|EC953729.1|EC953729
EST:     CCTATGGCTTCTTCCACAAAGGCCTCGTCCCTGGTCTCTGTTTTGGTGCA                         GGCCTTGGAATTACCGTGTTTGGAATGGCCTACATGTTTGTCCACGATGGT
genomic: CCTATGGCTTCTTCCACAAAGGCCTCGTCCCTGGTCTATGTTTTGGTGCAgtaagttcca ... ggttacacagGGCCTTGGAATTACCGTGTTTGGAATGGCCTACATGTTTGTCCACGATGGT
EST: gi|110422253|gb|EC988569.1|EC988569
EST:     CCTATGGCTTCTTCCACAAAGGCCTCGTCCCTGGTCTCTGTTTTGGTGCA                         GGCTTTGGAATTACCGTGTTTGGAATGGCCTACATGTTTGTCCACGATGGT
genomic: CCTATGGCTTCTTCCACAAAGGCCTCGTCCCTGGTCTATGTTTTGGTGCAgtaagttcca ... ggttacacagGGCCTTGGAATTACCGTGTTTGGAATGGCCTACATGTTTGTCCACGATGGT
EST: gi|110362556|gb|EC926099.1|EC926099
EST:     CCTATGGCTTCTTCCACAAAGGCCTCGTCCCTGGTCTCTGTTTTGGTGCA                         GGCCTTGGAATTACCGTGTTTGGAATGGCCTACATGTTTGTCCACGATGGT
genomic: CCTATGGCTTCTTCCACAAAGGCCTCGTCCCTGGTCTATGTTTTGGTGCAgtaagttcca ... ggttacacagGGCCTTGGAATTACCGTGTTTGGAATGGCCTACATGTTTGTCCACGATGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaaaaacaaaaacagtttaccttcagcttacaaaatcagtgtttggttacacagGGCCTTGGAATTACCGTGTTTGGAATGGCCTACATGTTTGTCCACGATGGTCTCGTCCACAGGAGATTTCCAGTGGGGCCCATTGCGAACGTGCCCTATT
                         agcttac  putative branch site (score: 3)
                            ttacaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttccatagtctcactgtacctattgattgatgactctgtgattagtgattactgattacagttcccaataattattttctatttttgaaaaacaaaaacagtttaccttcagcttacaaaatcagtgtttggttacacagGGCCTTGGAATTACCGTGTTTGGAATGGCCTACATGTTTGTCCACGATGGTCTCGTCCACAGGAGATTTCCAGTGGGGCCCATTGCGAACGTGCCCTATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT