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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatgttggcttatccatgttgttggtttgacagctcttctttctatctgatttccacctctttgcaatttattggagatcttgtttttctttccatacagGGATTACCGTGGCAATAGAATTGCCCTTTTTGATGGCATTGAGGAGGGTGGTATCAGGGCCTCATCTTCCTACTCCTCCCATGAAATAGATGAGCATGAT

Basic information

species Vitis vinifera
transcript Vv07s0005g02990.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0005g02990.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA03G31790.1 (Glycine max), 3'ss of exon 2
-----aatgttggcttatccatgttgttggtttgacagctcttctttctatctgatttccacctctttgcaatttattggagatcttgtttttctttcc-atacagGGATTACCGTGGCAATAGAATTGCCCTTTTTGATGGCATTGAGGAGGGTGGTATCAGGGCCTCATCTTCCTACTCCTC---CCATGAAATAGATGAGCATGAT
      || ||    | || |      || |   |  |   ||  | || | || | |  | |   |  | ||||  | |    |||||  || |||   ||  || ||  | |||  ||||||| || ||||||||||||| |||||||||||||| ||||| || ||||||   ||||||||    |||||||| ||||| |||   
cctgatattttaaactgtctagaactatg-tagaaaggaaatttatcctgtttg-tgtttatcatgtgaccatttggttg----cttgtacttgtttttgatctagAGACAATCGTAACAATAGAGTTTCCCTTTTTGATGGTATTGAGGAGGGTGGCATCAGAGCATCATCTGTTTACTCCTCTTCTCATGAAATTGATGAACAT---

upper sequence: Vv07s0005g02990.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA10G04020.1 (Glycine max), 3'ss of exon 2
aatgttggcttatccatgttgttggtttgacagctcttctttctatctgatttccacctctttgcaatttattggagatcttgtttttctttccata-cagGGATTACCGTGGCAATAGAATTGCCCTTTTTGATGGCATTGAGGAGGGTGGTATCAGGGCCTCATCTTCCTACTCCTCCCATGAAATAGATGAGCATGAT
| ||||    | || | |  ||     | |     | | | | |||    |  ||| ||     ||  |||  |         || |||||||  |  ||| |||   ||   ||| ||| |||| ||||||||||| |||||||||||||| ||||| || || |||   || |||||   |       ||||   ||||
actgttcaaatgtcta-gaagtgaaaattatcttgcatgtgtttattatctgaccatcttggctcatattaccgttttgtacattcttctttctgtttcagAGATGGTCGCAACAACAGAGTTGCTCTTTTTGATGGTATTGAGGAGGGTGGCATCAGAGCATCGTCTCTTTATTCCTCAAGTTCTTCCCATGAAATTGAT

upper sequence: Vv07s0005g02990.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA13G18170.2 (Glycine max), 3'ss of exon 2
--aatgttggcttatccatgttgttggtttgacagctcttctttctatctgatttccacctctttgcaatttattggagatcttgtttttctttccata-cagGGATTACCGTGGCAATAGAATTGCCCTTTTTGATGGCATTGAGGAGGGTGGTATCAGGGCCTCATCTTCCTACTCCTCCCATGAAATAGATGAGCATGAT
  |||||  | | |  |   |  |  || ||| |    |    | | |   | |   |  | | |    | ||||    |||||  | || ||||  |  ||| |||   |||  ||| ||| |||| ||||||||||| |||||||||||||| ||||| || || |||   ||||||||   |       ||||   ||||
gaaatgtcagatgactc---tgataagtctgaaactgttcaaatgtctagaagtgaaaattatcttgcttgtatttattatctttctattttttctgtttcagAGATGGTCGTAACAACAGAGTTGCTCTTTTTGATGGTATTGAGGAGGGTGGCATCAGAGCATCGTCTCTTTACTCCTCAACTTCTTCCCATGAAATTGAT

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|34549774|gb|CF518006.1|CF518006
EST:     GAATAGGCGGACAAGGGGAATCTGTGATCTCAATCCATGAATTCCAGAAG                         GGATTACCGTGGCAACAGAATTGCCCTTTTTGATGGCATTGAGGAGGGTGG
genomic: GAATAGGCGGACAAGGGGAATCTGTGATCTCAATCCATGAATTCCAGAAGgtttgttaat ... ttccatacagGGATTACCGTGGCAATAGAATTGCCCTTTTTGATGGCATTGAGGAGGGTGG
EST: gi|26257147|gb|CA808210.1|CA808210
EST:     GAATAGGCGGACAAGGGGAATCTGTGATCTCAATCCATGAATTCCAGAAG                         GGATTACCGTGGCAACAGAATTGCCCTCTTTGATGGCATTGAGGAGGGTGG
genomic: GAATAGGCGGACAAGGGGAATCTGTGATCTCAATCCATGAATTCCAGAAGgtttgttaat ... ttccatacagGGATTACCGTGGCAATAGAATTGCCCTTTTTGATGGCATTGAGGAGGGTGG
EST: gi|30306129|gb|CB982923.1|CB982923
EST:     GAATAGGCGGACAAGGGGAATCTGTGATCTCAATCCATGAATTCCAGAAG                         GGATTACCGTGGCAACAGAATTGCCCTTTTTGATGGCATTGAGGAGGGTGG
genomic: GAATAGGCGGACAAGGGGAATCTGTGATCTCAATCCATGAATTCCAGAAGgtttgttaat ... ttccatacagGGATTACCGTGGCAATAGAATTGCCCTTTTTGATGGCATTGAGGAGGGTGG
EST: gi|110371595|gb|EC935706.1|EC935706
EST:     GAATAGGCGGACAAGGGGAATCTGTGATCTCAATCCATGAATTCCAGAAG                         GGATTACCGTGGCAACAGAATTGCCCTTTTTGATGGCATTGAGGAGGGTGG
genomic: GAATAGGCGGACAAGGGGAATCTGTGATCTCAATCCATGAATTCCAGAAGgtttgttaat ... ttccatacagGGATTACCGTGGCAATAGAATTGCCCTTTTTGATGGCATTGAGGAGGGTGG
EST: gi|294964691|gb|GW838494.1|GW838494
EST:     GAATAGGCGGACAAGGGGAATCTGTGATCTCAATCCATGAATTCCAGAAG                         GGATTACCGTGGCAATAGAATTGCCCTTT
genomic: GAATAGGCGGACAAGGGGAATCTGTGATCTCAATCCATGAATTCCAGAAGgtttgttaat ... ttccatacagGGATTACCGTGGCAATAGAATTGCCCTTT
EST: gi|29782805|gb|CB348441.2|CB348441
EST:     GAATAGGCGGACAAGGGGAATCTGTGATCTCAATCCATGAATTCCAGAAG                         GGATTACCGTGGCAACAGAATTGCCCTTTTTGATGGCATTGAGGAGGGTGG
genomic: GAATAGGCGGACAAGGGGAATCTGTGATCTCAATCCATGAATTCCAGAAGgtttgttaat ... ttccatacagGGATTACCGTGGCAATAGAATTGCCCTTTTTGATGGCATTGAGGAGGGTGG
EST: gi|110708420|gb|EE085941.1|EE085941
EST:     GAATAGGTGGACAAGGGGAATCTGTGATCTCAATCCATGAATTCCAGAAG                         GGATTACCGTGGCAATAGAATTGCCCTTTTTGATGGCATTGAGGAGGGTGG
genomic: GAATAGGCGGACAAGGGGAATCTGTGATCTCAATCCATGAATTCCAGAAGgtttgttaat ... ttccatacagGGATTACCGTGGCAATAGAATTGCCCTTTTTGATGGCATTGAGGAGGGTGG
EST: gi|110405426|gb|EC970967.1|EC970967
EST:     GAATAGGCGGACAAGGGGAATCTGTGATCTCAATCCATGAATTCCAGAAG                         GGATTACCGTGGCAATAGAATTGCCCTTTTTGATGGCATTGAGGAGGGTGG
genomic: GAATAGGCGGACAAGGGGAATCTGTGATCTCAATCCATGAATTCCAGAAGgtttgttaat ... ttccatacagGGATTACCGTGGCAATAGAATTGCCCTTTTTGATGGCATTGAGGAGGGTGG
EST: gi|30306203|gb|CB982997.1|CB982997
EST:     GAATAGGCGGACAAGGGGAATCTGTGATCTCAATCCATGAATTCCAGAAG                         GGATTACCGTGGCAACAGAATTGCCCTTTTTGATGGCATTGAGGAGGGTGG
genomic: GAATAGGCGGACAAGGGGAATCTGTGATCTCAATCCATGAATTCCAGAAGgtttgttaat ... ttccatacagGGATTACCGTGGCAATAGAATTGCCCTTTTTGATGGCATTGAGGAGGGTGG
EST: gi|34550262|gb|CF518480.1|CF518480
EST:     GAATAGGCGGACAAGGGGAATCTGTGATCTCAATCCATGAATTCCAGAAG                         GGATCACCGTGGCAACAGAATTGCCCTTTTTGATGGCATTGAGGAGGGTGG
genomic: GAATAGGCGGACAAGGGGAATCTGTGATCTCAATCCATGAATTCCAGAAGgtttgttaat ... ttccatacagGGATTACCGTGGCAATAGAATTGCCCTTTTTGATGGCATTGAGGAGGGTGG
EST: gi|110724887|gb|EE101110.1|EE101110
EST:     GAATAGGCGGACAAGGGGAATCTGTGATCTCAATCCATGAATTCCAGAAG                         GGATTACCGTGGCAATAGAATTGCCCTTTTTGATGGCATTGAGGAGGGTGG
genomic: GAATAGGCGGACAAGGGGAATCTGTGATCTCAATCCATGAATTCCAGAAGgtttgttaat ... ttccatacagGGATTACCGTGGCAATAGAATTGCCCTTTTTGATGGCATTGAGGAGGGTGG
EST: gi|110378284|gb|EC943408.1|EC943408
EST:     GAATAGGCGGACAAGGGGAATCTGTGATCTCAATCCATGAATTCCAGAAG                         GGATTACCGTGGCAACAGAATTGCCCTTTTTGATGGCATTGAGGAGGGTGG
genomic: GAATAGGCGGACAAGGGGAATCTGTGATCTCAATCCATGAATTCCAGAAGgtttgttaat ... ttccatacagGGATTACCGTGGCAATAGAATTGCCCTTTTTGATGGCATTGAGGAGGGTGG
EST: gi|28969494|gb|CB348527.1|CB348527
EST:     GAATAGGCGGACAAGGGGAATCTGTGATCTCAATCCATGAATTCCAGAAG                         GGATTACCGTGGCAACAGAATTGCCCTTTTTGATGGCATTGAGGAGGGTGG
genomic: GAATAGGCGGACAAGGGGAATCTGTGATCTCAATCCATGAATTCCAGAAGgtttgttaat ... ttccatacagGGATTACCGTGGCAATAGAATTGCCCTTTTTGATGGCATTGAGGAGGGTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgatttccacctctttgcaatttattggagatcttgtttttctttccatacagGGATTACCGTGGCAATAGAATTGCCCTTTTTGATGGCATTGAGGAGGGTGGTATCAGGGCCTCATCTTCCTACTCCTCCCATGAAATAGATGAGCATGAT
 atctgat  putative branch site (score: 4)
                                 tcttgtttttctttcc  putative PPT
                    aatttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatgttggcttatccatgttgttggtttgacagctcttctttctatctgatttccacctctttgcaatttattggagatcttgtttttctttccatacagGGATTACCGTGGCAATAGAATTGCCCTTTTTGATGGCATTGAGGAGGGTGGTATCAGGGCCTCATCTTCCTACTCCTCCCATGAAATAGATGAGCATGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- tgttggc
- - - - - - -ccatgtt
- - - - - - - - - - - tggtttg
- - - - - - - - - - - - - - - cagctct