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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattccccttcattcctctcatgtagtagcataaatgaatacccctgtttggcattggtctcactgaataatcacaagacttgcacattgggtttcaccttgtccttgttacttggttctgattcttttaattgaattgttcgtgctttccaaaacagGGATCTTAACCAGTCGGAGAGAGCTAAGTATGGTATCCAGGACAACTTGGTTCGGTTCAGCTTTGGAGTTGAAGACTTTGAAGACTTGAAGGCTGACATA

Basic information

species Vitis vinifera
transcript Vv14s0108g01110.t01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0108g01110.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA09G37020.3 (Glycine max), 3'ss of exon 9
-----------------gtattc--cccttcattcctctcatgtag-tagcata-aatgaata--cccctgtttggcattggtctcactgaataatcaca--agacttgcacattgggtt--tcaccttgtccttgtt-acttggttctgattcttttaattgaattgttcgtgctttccaaaacagGGATCTTAACCAGTCGGAGAGAGCTAAGTATGGTATCCAGGACAACTTGGTTCGGTTCAGCTTTGGAGTTGAAGACTTTGAAGACTTGAAGGCTGACATA
                  | |||      ||||     | || | |  |  | | |  ||||   || ||  |||    ||  |     |   || ||       || |  | || ||||  | |   ||||   ||| || | ||| |  ||  ||||||| |||| |       ||    ||||||||||||   ||||| || || || |||||    ||  | |||||| ||||||| |||||||||||||||||||| ||||| || |||||||||||  | 
gtactcatttggattccatgttcaatttgtcatgttgatgattttgacactacacagggaatggtcctctacttgaatgtgaccctgtggtgaaagcatctttagctggtccttttggtttgttatagtgtcaaagtttaccttgtttttgttaatttaatttaattttcaacatattgtgcaacagGGATCTTCCTCAGTCAGAAAGGGCCAAGTACAAGATTTATGACAACCTGGTTCGCTTCAGCTTTGGAGTTGAAGATTTTGAGGATTTGAAGGCTGATGTC

upper sequence: Vv14s0108g01110.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA18G49660.1 (Glycine max), 3'ss of exon 10
gtattccccttcattcc---tctcatgtagtagcataaatgaat--acccctgtttggcattggtctc---actgaata---------atcacaagacttgcacattgggtttcaccttgtccttg-----ttacttggttctgattctt------ttaattgaattgttcgtgctttccaaaacagGGATCTTAACCAGTCGGAGAGAGCTAAGTATGGTATCCAGGACAACTTGGTTCGGTTCAGCTTTGGAGTTGAAGACTTTGAAGACTTGAAGGCTGACATA
||| ||   || |||||   | | | || ||    |  |||| |  || |   |  || | |||||       |||||          |    |||  |       |||   |    ||    ||      |  ||||||  || || ||      |||||| |||| |       ||    ||||||||||||   ||||| || || || ||||||   ||  | |||||| ||||||| |||||||||||||||||||| ||||| || |||||||||||  | 
gtactcatttttattccatgttttaagttgtcatgttgatgatttgacactactcggggaatggtcctctacttgaatgtgaccctgtagtgaaagcatcttttgctggtccttttgttaatttttagatttggcttggtggtggttgttgtatgtttaatttaattttcaacatattgtgcaacagGGATCTTCCTCAGTCAGAAAGGGCCAAGTATAAGATTTATGACAACCTGGTTCGCTTCAGCTTTGGAGTTGAAGATTTTGAGGATTTGAAGGCTGATGTC

upper sequence: Vv14s0108g01110.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: AT3G01120.1 (Arabidopsis thaliana), 3'ss of exon 10
gtattccccttcattcctctcatgtagtagcataaatgaatacccctgtttggcattggtctcactgaataatcacaagacttgcacattgggtttcaccttgtccttgttacttggttctgattcttttaattgaattgttcgtgctttccaaaacagGGATCTTAACCAGTCGGAGAGAGCTAAGTATGGTATCCAGGACAACTTGGTTCGGTTCAGCTTTGGAGTTGAAGACTTTGAAGACTTGAAGGCTGACATA
                                               || || | ||||    |  ||| ||    |    |    |  |  | |||     ||| |||  |          | | |   | ||  | ||   ||| |||  |   |||||||||    ||   |||||||   |||||||| ||| | || ||||||||||| |||||||||||||||||||||||||||||  | || |||||||| 
-----------------------------------------------gtatgtctttggcaaaatcgaacaaagttatctttgattccatatgcttc----cgtctttgacaaaatcgaacaaatttccgatttctaatgg--gtggttttgatttcagGGATCTGCCGCAAGAGGAGAGACTAAAGTATGGAATCAAAGATAACTTGGTTCGTTTCAGCTTTGGAGTTGAAGACTTTGAAGATGTCAAAGCTGACATT

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|28969813|gb|CB348846.1|CB348846
EST:     TTCGGAGGCTGTGAGAGCATTGTTGATCAGCCTGCGATTATGTCTTACTG                         GGATCTTAACCAGTCGG
genomic: TTCGGAGGCTGTGAGAGCATTGTTGATCAGCCTGCGATTATGTCTTACTGgtattcccct ... tccaaaacagGGATCTTAACCAGTCGG
EST: gi|110731786|gb|EE106500.1|EE106500
EST:     TTCGGAGGCTGTGAGAGCATTGTTGATCAGCCTGCGATTATGTCTTACTG                         GGATCTTAACCAGTCGGAGAGAGCTAAGTATGGTATCCAGGACAACTTGGT
genomic: TTCGGAGGCTGTGAGAGCATTGTTGATCAGCCTGCGATTATGTCTTACTGgtattcccct ... tccaaaacagGGATCTTAACCAGTCGGAGAGAGCTAAGTATGGTATCCAGGACAACTTGGT
EST: gi|110702814|gb|EE079112.1|EE079112
EST:     TTCGGAGGCTGTGAGAGCATTGTTGATCAGCCTGCGATTATGTCTTACTG                         GGATCTTAACCAGTCGGAAAGAGCTAATTATGGTATCCCGGACAACCTTGG
genomic: TTCGGAGGCTGTGAGAGCATTGTTGATCAGCCTGCGATTATGTCTTACTGgtattcccct ... tccaaaacagGGATCTTAACCAGTCGGAGAGAGCTAAGTATGGTATCCAGGACAAC-TTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccttgttacttggttctgattcttttaattgaattgttcgtgctttccaaaacagGGATCTTAACCAGTCGGAGAGAGCTAAGTATGGTATCCAGGACAACTTGGTTCGGTTCAGCTTTGGAGTTGAAGACTTTGAAGACTTGAAGGCTGACATA
                      ttttaat  putative branch site (score: 3)
                                        tgctttcc  putative PPT
                  attcttttaattgaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattccccttcattcctctcatgtagtagcataaatgaatacccctgtttggcattggtctcactgaataatcacaagacttgcacattgggtttcaccttgtccttgttacttggttctgattcttttaattgaattgttcgtgctttccaaaacagGGATCTTAACCAGTCGGAGAGAGCTAAGTATGGTATCCAGGACAACTTGGTTCGGTTCAGCTTTGGAGTTGAAGACTTTGAAGACTTGAAGGCTGACATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG