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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgcagtttaaaactcgcatttctccacaatccatagtccaaatgtttcctacattgaaaaatgaatctaaattatctttcatgacagGCAAAAAGATGATGTTGCAGGTGAAGTTCCTGTTGCATTTGTGGTTAGATCAAACGGGTTTGAACTCACTGAAGAGGCTGTGAAAGAGTTCATATCGAAA

Basic information

species Vitis vinifera
transcript Vv16s0039g02040.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0039g02040.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA01G44270.1 (Glycine max), 3'ss of exon 5
---------gtaagtgcagtttaaaactcgcatttctccacaatccatagtccaaatgtttcctacattgaaaaatgaatctaaattatctttcatgacagGCAAAAAGATGATGTTGCAGGTGAAGTTCCTGTTGCATTTGTGGTTAGATCAAACGGGTTTGAACTCACTGAAGAGGCTGTGAAAGAGTTCATATCGAAA
          |||    | ||| ||   |  |||  |   || |  |||||  | |||  |     | |||  ||| ||| | |   || | | |  |||| ||||| |||| || ||| ||||||||||||||||| || || || ||||||||||| ||||| || |||||||||||||| |||||||| ||| | |||
gtaagcttcttaatctgaattttaatggcttattattgtgca-tatatagtggacatgactgactgactgactaat-aattttatcaatatgtta--acagACAAAAGGATGTTGCTGCTGGTGAAGTTCCTGTTGCCTTCGTTGTGAGATCAAACGGCTTTGATCTAACTGAAGAGGCTGTAAAAGAGTTTATAGCTAAA

upper sequence: Vv16s0039g02040.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA11G01240.1 (Glycine max), 3'ss of exon 5
gtaagtgcagtttaaaactcgcatttctccacaatccatagtccaaatgtttcctacattgaaaaatgaatctaaattatctt----tcatgacagGCAAAAAGATGATGTTGCAGGTGAAGTTCCTGTTGCATTTGTGGTTAGATCAAACGGGTTTGAACTCACTGAAGAGGCTGTGAAAGAGTTCATATCGAAA
|||||     || | ||   | ||||    |   |  || || || || |     ||||     | ||| |   |||| | |     |  | |||| ||||| |||| || ||| ||||||||||||||||| || || || ||||||||||| ||||| || |||||||||||||| |||||||| ||| | |||
gtaagcttc-ttaataatctgaatttta--atggtttattgtgcatatatagtggacatgactgactgactaataattttatcaatatgttaacagACAAAAGGATGTTGCTGCTGGTGAAGTTCCTGTTGCCTTCGTTGTGAGATCAAACGGCTTTGATCTAACTGAAGAGGCTGTAAAAGAGTTTATAGCTAAA
















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|352773444|gb|FQ472226.1|FQ472226
EST:     GAGGCCCTTCTGGTGAGTCACCCATCAATTGCTGATGCAGCTGTTGTCCC                         GCAAAAAGATGATGTTGCAGGTGAAGTTCCTGTTGCATTTGTGGTTAGATC
genomic: GAGGCCCTTCTGGTGAGTCACCCATCAATTGCTGATGCAGCTGTTGTCCCgtaagtgcag ... ttcatgacagGCAAAAAGATGATGTTGCAGGTGAAGTTCCTGTTGCATTTGTGGTTAGATC
EST: gi|110425483|gb|EC991868.1|EC991868
EST:     GAGGCCCTTCTGGTGAGCCACCCATCAATTGCCGATGCAGCTGTTGTCCC                         GCAAAAAGATGATGTTGCGGGTGAAGTTCCTGTTGCATTTGTGGTTAGATC
genomic: GAGGCCCTTCTGGTGAGTCACCCATCAATTGCTGATGCAGCTGTTGTCCCgtaagtgcag ... ttcatgacagGCAAAAAGATGATGTTGCAGGTGAAGTTCCTGTTGCATTTGTGGTTAGATC
EST: gi|110699052|gb|EE077254.1|EE077254
EST:     GAGGCCCTTCTGGTGAGCCACCCATCAATTGCCGATGCAGCTGTTGTCCC                         GCAAAA-GATGATGTTGCGGGTGAAGTTCCTGTTGCATTTGTGGTTAGATC
genomic: GAGGCCCTTCTGGTGAGTCACCCATCAATTGCTGATGCAGCTGTTGTCCCgtaagtgcag ... ttcatgacagGCAAAAAGATGATGTTGCAGGTGAAGTTCCTGTTGCATTTGTGGTTAGATC
EST: gi|110422395|gb|EC988717.1|EC988717
EST:     GAGGCCCTTCTGGTGAGCCACCCATCAATTGCCGATGCAGCTGTTGTCCC                         GCAAAAAGATGATGTTGCGGGTGAAGTTCCTGTTGCATTTGTGGTTAGATC
genomic: GAGGCCCTTCTGGTGAGTCACCCATCAATTGCTGATGCAGCTGTTGTCCCgtaagtgcag ... ttcatgacagGCAAAAAGATGATGTTGCAGGTGAAGTTCCTGTTGCATTTGTGGTTAGATC
EST: gi|33404900|gb|CF210527.1|CF210527
EST:     GAGGCCCTTCTGGTGAGCCACCCATCAATTGCCGATGCAGCTGTTGTCCC                         GCAAAAAGATGATGTTGCGGGTGAAGTTCCTGTTGCATTTG
genomic: GAGGCCCTTCTGGTGAGTCACCCATCAATTGCTGATGCAGCTGTTGTCCCgtaagtgcag ... ttcatgacagGCAAAAAGATGATGTTGCAGGTGAAGTTCCTGTTGCATTTG
EST: gi|110699199|gb|EE075988.1|EE075988
EST:     GAGGCCCTTCTGGTGAGCCACCCATCAATTGCCGATGCAGCTGTTGTCCC                         GCAAAAAGATGATGCTGCGGGGGAAGTTCCTGTTGCATTTGGGGTTAGATC
genomic: GAGGCCCTTCTGGTGAGTCACCCATCAATTGCTGATGCAGCTGTTGTCCCgtaagtgcag ... ttcatgacagGCAAAAAGATGATGTTGCAGGTGAAGTTCCTGTTGCATTTGTGGTTAGATC
EST: gi|110361934|gb|EC925440.1|EC925440
EST:     GAGGCCCTTCTGGTGAGCCACCCATCAATTGCCGATGCAGCTGTTGTCCC                         GCAAAAAGATGATGTTGCGGGTGAAGTTCCTGTTGCATTTGTGGTTAGATC
genomic: GAGGCCCTTCTGGTGAGTCACCCATCAATTGCTGATGCAGCTGTTGTCCCgtaagtgcag ... ttcatgacagGCAAAAAGATGATGTTGCAGGTGAAGTTCCTGTTGCATTTGTGGTTAGATC
EST: gi|349826724|gb|FQ418815.1|FQ418815
EST:     GAGGCCCTTCTGGTGAGTCACCCATCAATTGCTGATGCAGCTGTTGTCCC                         GCAAAAAGATGATGTTGCAGGTGAAGTTCCTGTTGCATTTGTGGTTAGATC
genomic: GAGGCCCTTCTGGTGAGTCACCCATCAATTGCTGATGCAGCTGTTGTCCCgtaagtgcag ... ttcatgacagGCAAAAAGATGATGTTGCAGGTGAAGTTCCTGTTGCATTTGTGGTTAGATC
EST: gi|110384288|gb|EC948716.1|EC948716
EST:     GAGGCCCTTCTGGTGAGCCACCCATCAATTGCCGATGCAGCTGTTGTCCC                         GCAAAAAGATGATGTTGCGGGTGAAGTTCCTGTTGCATTTGTGGTTAGATC
genomic: GAGGCCCTTCTGGTGAGTCACCCATCAATTGCTGATGCAGCTGTTGTCCCgtaagtgcag ... ttcatgacagGCAAAAAGATGATGTTGCAGGTGAAGTTCCTGTTGCATTTGTGGTTAGATC
EST: gi|110388697|gb|EC953474.1|EC953474
EST:     GAGGCCCTTCTGGTGAGCCACCCATCAATTGCCGATGCAGCTGTTGTCCC                         GCAAAAAGATGATGTTGCGGGTGAAGTTCCTGTTGCATTTGTGGTTAGATC
genomic: GAGGCCCTTCTGGTGAGTCACCCATCAATTGCTGATGCAGCTGTTGTCCCgtaagtgcag ... ttcatgacagGCAAAAAGATGATGTTGCAGGTGAAGTTCCTGTTGCATTTGTGGTTAGATC
EST: gi|352768957|gb|FQ468148.1|FQ468148
EST:     GAGGCCCTTCTGGTGAGTCACCCATCAATTGCTGATGCAGCTGTTGTCCC                         GCAAAAAGATGATGTTGCAGGTGAAGTTCCTGTTGCATTTGTGGTTAGATC
genomic: GAGGCCCTTCTGGTGAGTCACCCATCAATTGCTGATGCAGCTGTTGTCCCgtaagtgcag ... ttcatgacagGCAAAAAGATGATGTTGCAGGTGAAGTTCCTGTTGCATTTGTGGTTAGATC
EST: gi|33404985|gb|CF210612.1|CF210612
EST:     GAGGCCCTTCTGGTGAGCCACCCATCAATTGCCGATGCAGCTGTTGTCCC                         GCAAAAAGATGATGTTGCGGGTGAAGTTCCTGTTGCATTTGTGGTTAGATC
genomic: GAGGCCCTTCTGGTGAGTCACCCATCAATTGCTGATGCAGCTGTTGTCCCgtaagtgcag ... ttcatgacagGCAAAAAGATGATGTTGCAGGTGAAGTTCCTGTTGCATTTGTGGTTAGATC
EST: gi|110376549|gb|EC941609.1|EC941609
EST:     GAGGCCCTTCTGGTGAGCCACCCATCAATTGCCGATGCAGCTGTTGTCCC                         GCAAAAAGATGATGTTGCGGGTGAAGTTCCTGTTGCATTTGTGGTTAGATC
genomic: GAGGCCCTTCTGGTGAGTCACCCATCAATTGCTGATGCAGCTGTTGTCCCgtaagtgcag ... ttcatgacagGCAAAAAGATGATGTTGCAGGTGAAGTTCCTGTTGCATTTGTGGTTAGATC
EST: gi|110362812|gb|EC926367.1|EC926367
EST:     GAGGCCCTTCTGGTGAGCCACCCATCAATTGCCGATGCAGCTGTTGTCCC                         GCAAAAAGATGATGTTGCGGGTGAAGTTCCTGTTGCATTTGTGGTTAGATC
genomic: GAGGCCCTTCTGGTGAGTCACCCATCAATTGCTGATGCAGCTGTTGTCCCgtaagtgcag ... ttcatgacagGCAAAAAGATGATGTTGCAGGTGAAGTTCCTGTTGCATTTGTGGTTAGATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atagtccaaatgtttcctacattgaaaaatgaatctaaattatctttcatgacagGCAAAAAGATGATGTTGCAGGTGAAGTTCCTGTTGCATTTGTGGTTAGATCAAACGGGTTTGAACTCACTGAAGAGGCTGTGAAAGAGTTCATATCGAAA
                                atctaaa  putative branch site (score: 3)
                                       ttatctttc  CT-rich tract
                    attgaaaaatgaatct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgcagtttaaaactcgcatttctccacaatccatagtccaaatgtttcctacattgaaaaatgaatctaaattatctttcatgacagGCAAAAAGATGATGTTGCAGGTGAAGTTCCTGTTGCATTTGTGGTTAGATCAAACGGGTTTGAACTCACTGAAGAGGCTGTGAAAGAGTTCATATCGAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG