Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattcttcgcctccttcaactagagtcgaaccatatagtccctataatgatgggtttccattcgaattctactaataaacttaccctttttgtttgtctgaattccatctttgttcaaacaaattagctaatgaactatttcttaaactcttttatgcagCTCGATTCTCTGAAGCCAAAGGAGAGCTTGGTGATGAGACAGAGATATGGTCTTGATGGTAAGGGTGATCGGACACTGGGGGAGATTGCAGGAAACCTAA

Basic information

species Vitis vinifera
transcript Vv16s0050g02520.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0050g02520.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA06G13100.3 (Glycine max), 3'ss of exon 5
gtaattcttcgcctccttcaactagagtcgaaccatatagtccctataatgatgggtttccattcgaattctactaataaacttaccctttttgtt-tgtctgaattccatctttgttcaaacaaattagctaatgaactatttcttaaactcttttatgcagCTCGATTCTCTGAAGCCAAAGGAGAGCTTGGTGATGAGACAGAGATATGGTCTTGATGGTAAGGGTGATCGGACACTGGGGGAGATTGCAGGAAACCTAA
                                                          |    | |  |  || ||||| |  ||      ||  |   ||    | ||||  |  || |  ||| | | || | ||  | ||| ||    | |||||   |||| ||||| |||||||| ||||||||||||||||| |||||||||| ||| |||||||| ||||||||  | ||| |||| || ||||| || ||| | |
----------------------------------------------------------ttttctagtttgttagtaatatatctaattcaattactacatcatgttgccatgatcatttatgcaactaatctga-gatttttttttt---tttttttac-tagCTTGATTCCCTGAAGCCGAAGGAGAGCTTGGTGATCAGACAGAGATTTGGACTTGATGGCAAGGGTGACAGAACATTGGGAGAAATTGCTGGGAACTTGA

upper sequence: Vv16s0050g02520.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA14G31370.1 (Glycine max), 3'ss of exon 5
gtaattcttcgcctccttcaactagagtcgaaccatatagtccctataatgatgggtttccattcgaattctactaataaacttaccctttttgtttgtctgaattccatctttgttcaaacaaattagctaatgaactatttcttaaactcttttatgcagCTCGATTCTCTGAAGCCAAAGGAGAGCTTGGTGATGAGACAGAGATATGGTCTTGATGGTAAGGGTGATCGGACACTGGGGGAGATTGCAGGAAACCTAA
                                                             |||      | || |  ||||  || | |  |   ||  |    |  | |  |     || |     | |  | ||   || ||  |  | |||| |  |||| |||||  ||||||||||||||||| | ||||| |||||||||||||| |||||||| ||||||||  ||||| |||| || || || || ||| | |
-------------------------------------------------------------atttaggcgc-acgacaaaacaaacacatgcttggtgatttttctataaccataacataatattgatgtttctaaaaatttcctggattttttttttctagCTTGATTCCTTGAAGCCAAAGGAGAGCCTAGTGATCAGACAGAGATATGGACTTGATGGCAAGGGTGACAGGACATTGGGAGAAATCGCTGGGAACTTGA

upper sequence: Vv16s0050g02520.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA13G08390.1 (Glycine max), 3'ss of exon 4
gtaattcttcgcctccttcaactagagtcgaaccatatagtccctataatgatgggtttccattcgaattctactaataaacttaccctttttgtttgtctgaattccatctttgttcaaacaaattagctaatgaactatttcttaaactcttttatgcagCTCGATTCTCTGAAGCCAAAGGAGAGCTTGGTGATGAGACAGAGATATGGTCTTGATGGTAAGGGTGATCGGACACTGGGGGAGATTGCAGGAAACCTAA
                                                           | | |  | |  |  |||| || |     ||| | | | | |  ||   | || |  | |    ||||   |    ||  | ||||| || | |||     |||| ||||| |||||||||||||||||| | ||||| || ||||||||||| |||||||| ||||||||  | ||| |||| || ||||| || ||| | |
----------------------------------------------------------actaatttattggtcttaatgaattaggtatttgtttct-tatatataggaactatagtaattttaattttttttaaaaaaaattcttgaattttttc---tagCTTGATTCCCTGAAGCCAAAGGAGAGCCTAGTGATCAGGCAGAGATATGGACTTGATGGCAAGGGTGACAGAACATTGGGAGAAATTGCTGGGAACTTGA

upper sequence: Vv16s0050g02520.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA04G41690.1 (Glycine max), 3'ss of exon 3
gtaattcttcgcctccttcaactagagtcgaaccatatagtccctataatgatgggtttccattcgaattctactaataaacttaccctttttgtttgtctgaattccatctttgttcaaacaaattagctaatgaactatttcttaaactcttttatgcagCTCGATTCTCTGAAGCCAAAGGAGAGCTTGGTGATGAGACAGAGATATGGTCTTGATGGTAAGGGTGATCGGACACTGGGGGAGATTGCAGGAAACCTAA
                                                   |    ||||  || |  |  || ||||  |  ||      ||     ||  | | ||||     ||  | | || ||    ||||  | ||| ||       || |   |||| ||||| |||||||| ||||||||||||||||| |||||||||| ||| ||||| || ||||||||  | ||  |||| || ||||| || ||  | |
--------------------------------------------------taaaactttcgtttagtttgttagtaatgcatctaattcaattac--atcatattgccatgggcattttatccaactaat--atgagatttttttt-------ttcac-tagCTTGATTCCCTGAAGCCGAAGGAGAGCTTGGTGATCAGACAGAGATTTGGACTTGACGGCAAGGGTGACAGAACGTTGGGAGAAATTGCTGGGAATTTGA

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|45368264|gb|CK906623.1|CK906623
EST:     GTGATAGGGGGCGGCAACTTGCTCTTCTCAGACTTGCTCTTGATGATGTG                         CTCGATTCTCTGAAGCCAAAGGAGAGCTTGGTGATGAGACAGAGATATGGT
genomic: GTGATAGGGGGCGGCAACTTGCTCTTCTCAGACTTGCTCTTGATGATGTGgtaattcttc ... ttttatgcagCTCGATTCTCTGAAGCCAAAGGAGAGCTTGGTGATGAGACAGAGATATGGT
EST: gi|30135385|gb|CB920723.1|CB920723
EST:     GTGATAGGGGGCGGCAACTTGCTCTTCTCAGACTTGCTCTTGATGATGTG                         CTCGATTCTCTGAAGCCAAAGGAGAGCTTGGTGATGAGACAGAGATATGGT
genomic: GTGATAGGGGGCGGCAACTTGCTCTTCTCAGACTTGCTCTTGATGATGTGgtaattcttc ... ttttatgcagCTCGATTCTCTGAAGCCAAAGGAGAGCTTGGTGATGAGACAGAGATATGGT
EST: gi|34550585|gb|CF518803.1|CF518803
EST:     GTGATAGGGGGCGGCAACTTGCTCTTCTCAGACTTGCTCTTGATGATGTG                         CTCGATTCTCTGAAGCCAAAGGAGAGCTTGGTGATGAGACAGAGATATGGT
genomic: GTGATAGGGGGCGGCAACTTGCTCTTCTCAGACTTGCTCTTGATGATGTGgtaattcttc ... ttttatgcagCTCGATTCTCTGAAGCCAAAGGAGAGCTTGGTGATGAGACAGAGATATGGT
EST: gi|34363418|gb|CF405003.1|CF405003
EST:     GTGATAGGGGGCGGCAACTTGCTCTTCTCAGACTTGCTCTTGATGATGTG                         CTCGATTCTCTGAAGCCAAAGGAGAGCTTGGTGATGAGACAGAGATATGGT
genomic: GTGATAGGGGGCGGCAACTTGCTCTTCTCAGACTTGCTCTTGATGATGTGgtaattcttc ... ttttatgcagCTCGATTCTCTGAAGCCAAAGGAGAGCTTGGTGATGAGACAGAGATATGGT
EST: gi|28964721|gb|CB343754.1|CB343754
EST:     GTGATAGGGGGCGGCAACTTGCTCTTCTCAGACTTGCTCTTGATGATGTG                         CTCGATTCTCTGAAGCCAAAGGAGAGCTTGGTGATGAGACAGAGATATGGT
genomic: GTGATAGGGGGCGGCAACTTGCTCTTCTCAGACTTGCTCTTGATGATGTGgtaattcttc ... ttttatgcagCTCGATTCTCTGAAGCCAAAGGAGAGCTTGGTGATGAGACAGAGATATGGT
EST: gi|110375753|gb|EC940766.1|EC940766
EST:     GTGATAGGGGGCGGCAACTTGCTCTTCTCAGACTTGCTCTTGATGATGTG                         CTCGATTCTCTGAAGCCAAAGGAGAGCTTGGTGATGAGACAGAGATATGGT
genomic: GTGATAGGGGGCGGCAACTTGCTCTTCTCAGACTTGCTCTTGATGATGTGgtaattcttc ... ttttatgcagCTCGATTCTCTGAAGCCAAAGGAGAGCTTGGTGATGAGACAGAGATATGGT
EST: gi|34550673|gb|CF518891.1|CF518891
EST:     GTGATAGGGGGCGGCAACTTGCTCTTCTCAGACTTGCTCTTGATGATGTG                         CTCGATTCTCTGAAGCCAAAGGAGAGCTTGGTGATGAGACAGAGATATGGT
genomic: GTGATAGGGGGCGGCAACTTGCTCTTCTCAGACTTGCTCTTGATGATGTGgtaattcttc ... ttttatgcagCTCGATTCTCTGAAGCCAAAGGAGAGCTTGGTGATGAGACAGAGATATGGT
EST: gi|110719640|gb|EE094946.1|EE094946
EST:     GTGATANGGGGCGGCAACTTGCTCTTCTCAGACTTGCTCTTGATGATGTG                         CTTGATTCTCTGAAGCCAAAGGAGAGCTTGGTGATGAGACAGAGATATGGT
genomic: -TGATAGGGGGCGGCAACTTGCTCTTCTCAGACTTGCTCTTGATGATGTGgtaattcttc ... ttttatgcagCTCGATTCTCTGAAGCCAAAGGAGAGCTTGGTGATGAGACAGAGATATGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catctttgttcaaacaaattagctaatgaactatttcttaaactcttttatgcagCTCGATTCTCTGAAGCCAAAGGAGAGCTTGGTGATGAGACAGAGATATGGTCTTGATGGTAAGGGTGATCGGACACTGGGGGAGATTGCAGGAAACCTAA
                    agctaat  putative branch site (score: 3)
                                          ctcttttat  putative PPT
                            aactatttcttaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattcttcgcctccttcaactagagtcgaaccatatagtccctataatgatgggtttccattcgaattctactaataaacttaccctttttgtttgtctgaattccatctttgttcaaacaaattagctaatgaactatttcttaaactcttttatgcagCTCGATTCTCTGAAGCCAAAGGAGAGCTTGGTGATGAGACAGAGATATGGTCTTGATGGTAAGGGTGATCGGACACTGGGGGAGATTGCAGGAAACCTAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT