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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttcttaaatctgtgtgtgtgtgtgtgtgtgtgtcacatgcatgtactcctcaccttattgtttaatttctatcggtaccttgttttacaagtacctaccccatttgcttgcagGAAAAAGTTAATGTGCATGGTGGTGCTGTATCCTTGGGACATCCTCTAGGTTGCAGTGGAGCCCGAATCTTGGTCACACTTTTGGGG

Basic information

species Vitis vinifera
transcript Vv12s0057g01200.t01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0057g01200.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: LOC_Os09g07830.3 (Oryza sativa), 3'ss of exon 11
----------------------------------------gtgagttcttaaatctgtgtgtgtgtgtgtgtgtgtgtcacatgca-----tgtactcct----caccttattgtttaatttc-tatcggtaccttgttttacaagtacctaccc--catttgct--tgcagGAAAAAGTTAATGTGCATGGTGGTGCTGTATCCTTGGGACATCCTCTAGGTTGCAGTGGAGCCCGAATCTTGGTCACACTTTTGGGG
                                         |   || ||||||   | |  |    ||  | |  ||  | | ||     || | | |     ||   | | || |       |||   |   ||  ||    | |||    |    |||||||  || |||||||| ||||||| ||||| || ||||| || || ||||||||||| || |||||||| || ||||| |||||||| ||  | || 
gtaagctgccttagttcaactataattatttctggaactaattgttttttaaattgttcttggaaattgcatttaagttcccttcactatttgaaattcgctggcaatctttagtgtggcccaatatttatgtattagttccttaatactctgctggtatttgctcctgtagGAAAAAATTAATGTACATGGAGGAGCTGTGTCTTTAGGACATCCTCTTGGATGCAGTGGTGCTCGAATTTTGGTCACCCTGCTTGGT

upper sequence: Vv12s0057g01200.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GRMZM5G866758_T02 (Zea mays), 3'ss of exon 12
----------------------------------------------gtgagttcttaaatctgtgtgtgtgtgtgtgtgtgtgtcacatgc-atgtactcctcacct-tattgtttaatttctatcggtaccttgttttacaagtacctaccccatttgcttgcagGAAAAAGTTAATGTGCATGGTGGTGCTGTATCCTTGGGACATCCTCTAGGTTGCAGTGGAGCCCGAATCTTGGTCACACTTTTGGGG
                                              || |     | | | |  |   ||   | | ||| | |    ||  || | ||   || |   |  || ||||| | ||    ||  | || |          | |  || || |||||||||||  ||||||| ||||| || ||||||||||| ||||||||||| || |||||||| || || || ||||| || ||| | || 
gtaagtgtcacctgtattaaactgccattctttgtggattttagaagttaaacaatcactttcagaaagtacatat-tgtctcttttttgttatttgctatgcagcagcaacgtgtaattgc-attataacagtattatctgtactaacagcatatgtgtttgcagGAAAAGATTAATGTTCATGGAGGAGCTGTATCCTTAGGACATCCTCTCGGGTGCAGTGGTGCTCGCATTTTGGTTACCCTTATTGGT

upper sequence: Vv12s0057g01200.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GRMZM5G830250_T01 (Zea mays), 3'ss of exon 10
---------------gtgagttcttaaatctgtgtg---tgtgtgtgtgtgtgtgtcacatgcatgtac--tcctcaccttattgtttaatttctatcggtaccttgt------tttacaa--gtacctaccccatt-----------tgcttgcagGAAAAAGTTAATGTGCATGGTGGTGCTGTATCCTTGGGACATCCTCTAGGTTGCAGTGGAGCCCGAATCTTGGTCACACTTTTGGGG
                  |       | ||| ||||   | |    ||       |||| | ||| | |  ||   |  || || |||  | |  | | | | | |||       | ||||  |||    | | | |           ||| ||||||||||   |||||| |||||||| |||||||| || ||||||||||| || |||||||| || || || |||               
gtaagtgtcatctttactaaactaccattctttgtggattttaaaagtcaaaacatcactttcatatgcattcgctatttttttatttgctatgcagcagcaacatgtaatcgcatgacaatagtattctctctactaacggtatatgtgcgtgcagGAAAAGACTAATGTTCATGGTGGAGCTGTATCTTTAGGACATCCTCTTGGGTGCAGTGGTGCTCGCATTTTG---------------

upper sequence: Vv12s0057g01200.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA14G00760.2 (Glycine max), 3'ss of exon 9
gtgagttcttaaatctgtgtgtgtgtgtgtgtgtgtgtcacatgcatgtactcctcaccttattgtttaatttctatcggtaccttgttttacaagtacctaccccatttgcttgcagGAAAAAGTTAATGTGCATGGTGGTGCTGTATCCTTGGGACATCCTCTAGGTTGCAGTGGAGCCCGAATCTTGGTCACACTTTTGGGG
        | |||| ||| | |   |   |   |      |||   |||   | | |    ||        ||| ||   |  ||| || | |||||| |||     ||   |||||||||||||| || || |||||||| |||||  |  |||| |||||||| ||||||||||| || || ||  |||| ||||||||||||
------gttaaaatttgtctata-atccataatttaacttcat---tgtgaccattaatggatgtacc--cttccatttatttctttttct-caagtaacta-----ttattttgcagGAAAAAGTAAACGTACATGGTGGAGCTGTTGCACTGGGTCATCCTCTTGGTTGCAGTGGTGCTCGCATTCTGGTGACACTTTTGGGG

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|352790687|gb|FQ475445.1|FQ475445
EST:     GTTGTGGCTCTTGCAAATCAGAAACTGCTTGGACTTAGTCCC                         GAAAAAGTTAATGTGCATGGTGGTGCTGTATCCTTGGGACATCCTCTAGGT
genomic: GTTGTGGCTCTTGCAAATCAGAAACTGCTTGGACTTAGTCCCgtgagttctt ... ttgcttgcagGAAAAAGTTAATGTGCATGGTGGTGCTGTATCCTTGGGACATCCTCTAGGT
EST: gi|30130059|gb|CB915398.1|CB915398
EST:     GTTGTGGCTCTTGCAAATCAGAAACTGCTTGGACTTAGTCCC                         GAAAAAGTTAATGTGCATGGTGGTGCTGTATCCTTGGGACATCCTCTAGGT
genomic: GTTGTGGCTCTTGCAAATCAGAAACTGCTTGGACTTAGTCCCgtgagttctt ... ttgcttgcagGAAAAAGTTAATGTGCATGGTGGTGCTGTATCCTTGGGACATCCTCTAGGT
EST: gi|71876405|gb|DT025460.1|DT025460
EST:     GTTGTGGCTCTTGCAAATCAGAAACTGCTTGGACTTAGTCCC                         GAAAAAGTTAATGTGCATGGTGGTGCTGTATCCTTGGGACATCCTCTAGGT
genomic: GTTGTGGCTCTTGCAAATCAGAAACTGCTTGGACTTAGTCCCgtgagttctt ... ttgcttgcagGAAAAAGTTAATGTGCATGGTGGTGCTGTATCCTTGGGACATCCTCTAGGT
EST: gi|30129594|gb|CB914933.1|CB914933
EST:     GTTGTGGCTCTTGCAAATCAGAAACTGCTTGGACTTAGTCCC                         GAAAAAGTTAATGTGCATGGTGGTGCTGTATCCTTGGGACATCCTCTAGGT
genomic: GTTGTGGCTCTTGCAAATCAGAAACTGCTTGGACTTAGTCCCgtgagttctt ... ttgcttgcagGAAAAAGTTAATGTGCATGGTGGTGCTGTATCCTTGGGACATCCTCTAGGT
EST: gi|110700654|gb|EE077500.1|EE077500
EST:     GTTGTGGCTCTTGCAAATCAGAAACTGCTTGGACTTAGTCCC                         GAAAAA-TTAATGTGCATGGTGGTGCTGTATCCTTGGGACATCCTCTAGGT
genomic: GTTGTGGCTCTTGCAAATCAGAAACTGCTTGGACTTAGTCCCgtgagttctt ... ttgcttgcagGAAAAAGTTAATGTGCATGGTGGTGCTGTATCCTTGGGACATCCTCTAGGT
EST: gi|349833317|gb|FQ416695.1|FQ416695
EST:     GTTGTGGCTCTTGCAAATCAGAAACTGCTTGGACTTAGTCCC                         GAAAAAGTTAATGTGCATGGTGGTGCTGTATCCTTNGGACATCCTCTAGGT
genomic: GTTGTGGCTCTTGCAAATCAGAAACTGCTTGGACTTAGTCCCgtgagttctt ... ttgcttgcagGAAAAAGTTAATGTGCATGGTGGTGCTGTATCCTTGGGACATCCTCTAGGT
EST: gi|110368276|gb|EC932247.1|EC932247
EST:     GTTGTGGCTCTTGCAAATCAGAAACTGCTTGGACTTAGTCCC                         GAAAAAGTTAATGTGCATGGTGGTGCTGTATCCTTGGGACATCCTCTAGGT
genomic: GTTGTGGCTCTTGCAAATCAGAAACTGCTTGGACTTAGTCCCgtgagttctt ... ttgcttgcagGAAAAAGTTAATGTGCATGGTGGTGCTGTATCCTTGGGACATCCTCTAGGT
EST: gi|110371396|gb|EC935385.1|EC935385
EST:     GTTGTGGCTCTTGCAAATCAGAAACTGCTTGGACTTAGTCCC                         GAAAAAGTTAATGTGCATGGTGGTGCTGTATCCTTGGGACATCCTCTAGGT
genomic: GTTGTGGCTCTTGCAAATCAGAAACTGCTTGGACTTAGTCCCgtgagttctt ... ttgcttgcagGAAAAAGTTAATGTGCATGGTGGTGCTGTATCCTTGGGACATCCTCTAGGT
EST: gi|27584750|gb|CB007445.1|CB007445
EST:     GTTGTGGCTCTTGCAAATCAGAAACTGCTTGGACTTAGTCCC                         GAAAAAGTTAATGTGCATGGTGGTGCTGTATCCTTGGGACATCCTCTAGGT
genomic: GTTGTGGCTCTTGCAAATCAGAAACTGCTTGGACTTAGTCCCgtgagttctt ... ttgcttgcagGAAAAAGTTAATGTGCATGGTGGTGCTGTATCCTTGGGACATCCTCTAGGT
EST: gi|33402805|gb|CF208432.1|CF208432
EST:     GTTGTGGCTCTTGCAAATCAGAAACTGCTTGGACTTAGTCCC                         GAAAAAGTTAATGTGCATGGTGGTGCTGTATCCTTGGGACATCCTCTAGGT
genomic: GTTGTGGCTCTTGCAAATCAGAAACTGCTTGGACTTAGTCCCgtgagttctt ... ttgcttgcagGAAAAAGTTAATGTGCATGGTGGTGCTGTATCCTTGGGACATCCTCTAGGT
EST: gi|110361968|gb|EC925474.1|EC925474
EST:     GTTGTGGCTCTTGCAAATCAGAAACTGCTTGGACTTAGTCCC                         GAAAAAGTTAATGTGCATGGTGGTGCTGTATCCTTGGGACATCCTCTAGGT
genomic: GTTGTGGCTCTTGCAAATCAGAAACTGCTTGGACTTAGTCCCgtgagttctt ... ttgcttgcagGAAAAAGTTAATGTGCATGGTGGTGCTGTATCCTTGGGACATCCTCTAGGT
EST: gi|30133750|gb|CB919089.1|CB919089
EST:     GTTGTGGCTCTTGCAAATCAGAAACTGCTTGGACTTAGTCCC                         GAAAAAGTTAATGTGCATGGTGGTGCTGTATCCTTGGGACATCCTCTAGGT
genomic: GTTGTGGCTCTTGCAAATCAGAAACTGCTTGGACTTAGTCCCgtgagttctt ... ttgcttgcagGAAAAAGTTAATGTGCATGGTGGTGCTGTATCCTTGGGACATCCTCTAGGT
EST: gi|26259676|gb|CA810739.1|CA810739
EST:     GTTGTGGCTCTTGCAAATCAGAAACTGCTTGGACTTAGTCCC                         GAAAAAGTTAATGTGCATGGTGGTGCTGTATCCTTGGGACATCCTCTAGGT
genomic: GTTGTGGCTCTTGCAAATCAGAAACTGCTTGGACTTAGTCCCgtgagttctt ... ttgcttgcagGAAAAAGTTAATGTGCATGGTGGTGCTGTATCCTTGGGACATCCTCTAGGT
EST: gi|110361336|gb|EC924802.1|EC924802
EST:     GTTGTGGCTCTTGCAAATCAGAAACTGCTTGGACTTAGTCCC                         GAAAAAGTTAATGTGCATGGTGGTGCTGTATCCTTGGGACATCCTCTAGGT
genomic: GTTGTGGCTCTTGCAAATCAGAAACTGCTTGGACTTAGTCCCgtgagttctt ... ttgcttgcagGAAAAAGTTAATGTGCATGGTGGTGCTGTATCCTTGGGACATCCTCTAGGT
EST: gi|110362059|gb|EC925566.1|EC925566
EST:     GTTGTGGCTCTTGCAAATCAGAAACTGCTTGGACTTAGTCCC                         GAAAAAGTTAATGTGCATGGTGGTGCTGTATCCTTGGGACATCCTCTAGGT
genomic: GTTGTGGCTCTTGCAAATCAGAAACTGCTTGGACTTAGTCCCgtgagttctt ... ttgcttgcagGAAAAAGTTAATGTGCATGGTGGTGCTGTATCCTTGGGACATCCTCTAGGT
EST: gi|110357331|gb|EC920800.1|EC920800
EST:     GTTGTGGCTCTTGCAAATCAGAAACTGCTTGGACTTAGTCCC                         GAAAAAGTTAATGTGCATGGTGGTGCTGTATCCTTGGGACATCCTCTAGGT
genomic: GTTGTGGCTCTTGCAAATCAGAAACTGCTTGGACTTAGTCCCgtgagttctt ... ttgcttgcagGAAAAAGTTAATGTGCATGGTGGTGCTGTATCCTTGGGACATCCTCTAGGT
EST: gi|32246227|gb|CD712046.1|CD712046
EST:     GTTGTGGCTCTTGCAAATCAGAAACTGCTTGGACTTAGTCCC                         GAAAAAGTTAATGTGCATGGTGGTGCTGTATCCTTGGGACATCCTTTAGGT
genomic: GTTGTGGCTCTTGCAAATCAGAAACTGCTTGGACTTAGTCCCgtgagttctt ... ttgcttgcagGAAAAAGTTAATGTGCATGGTGGTGCTGTATCCTTGGGACATCCTCTAGGT
EST: gi|33403297|gb|CF208924.1|CF208924
EST:     GTTGTGGCTCTTGCAAATCAGAAACTGCTTGGACTTAGTCCC                         GAAAAAGTTAATGTGCATGGTGGTGCTGTATCCTTGGGACATCCTCTAGGT
genomic: GTTGTGGCTCTTGCAAATCAGAAACTGCTTGGACTTAGTCCCgtgagttctt ... ttgcttgcagGAAAAAGTTAATGTGCATGGTGGTGCTGTATCCTTGGGACATCCTCTAGGT
EST: gi|110723122|gb|EE100072.1|EE100072
EST:     GTTGTGGCTCTTGCAAATCAGAAACTGCTTGGACTTAGTCCC                         GAAAAAGTTAATGTGCATGGTGGTGCTGTATCCTTGGGACATCCTCTAGGT
genomic: GTTGTGGCTCTTGCAAATCAGAAACTGCTTGGACTTAGTCCCgtgagttctt ... ttgcttgcagGAAAAAGTTAATGTGCATGGTGGTGCTGTATCCTTGGGACATCCTCTAGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtttaatttctatcggtaccttgttttacaagtacctaccccatttgcttgcagGAAAAAGTTAATGTGCATGGTGGTGCTGTATCCTTGGGACATCCTCTAGGTTGCAGTGGAGCCCGAATCTTGGTCACACTTTTGGGG
 gtttaat  putative branch site (score: 4)
                                       ccccattt  putative PPT
     aatttctat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagttcttaaatctgtgtgtgtgtgtgtgtgtgtgtcacatgcatgtactcctcaccttattgtttaatttctatcggtaccttgttttacaagtacctaccccatttgcttgcagGAAAAAGTTAATGTGCATGGTGGTGCTGTATCCTTGGGACATCCTCTAGGTTGCAGTGGAGCCCGAATCTTGGTCACACTTTTGGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG