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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catgtatgttctataatatgtggtttgaatgtttgtgttttagttttctgagagaaaattgcttgaaacttttgttttggtgggctggtttctttgacagATATGCCTCAATTAGGGCAATTGAGACCAAGTCCCCTGTTGATGATCAGCAATGGCTCACATACTGGGTTTTGTATTCTATGATCACACTCTTCGAGCTC

Basic information

species Vitis vinifera
transcript Vv17s0000g05990.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g05990.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os06g12220.1 (Oryza sativa), 3'ss of exon 2
catgtatgttctataatat-gtggtttga-atgtttgtgttttagttttctgagagaaaattgcttgaaacttttgttttggtgggctggtttctttgacagATATGCCTCAATTAGGGCAATTGAGACCAAGTCCCCTGTTGATGATCAGCAATGGCTCACATACTGGGTTTTGTATTCTATGATCACACTCTTCGAGCTC
   ||| ||  |||  | | ||  ||  | || ||    ||||  || | |||       |    | | |  | | | |   |    |     |||   ||||||||||||  | || ||||| || || || || |||||||||||||||||||||||||| ||||||||  |||| ||  | |||||  | || ||||| 
---gtaagtattattttgttgtaattcaatattttgccattttgattgtttgattatttctgttattatatatatatatatttacttttcgcacttctgcagATATGCCTCTGTGAGAGCAATAGAAACAAAATCTCCTGTTGATGATCAGCAATGGCTCACTTACTGGGTGCTGTACTCGTTTATCACTTTGTTTGAGCTT

upper sequence: Vv17s0000g05990.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os02g51290.2 (Oryza sativa), 3'ss of exon 2
catgtatgttctataatatgtggtttgaatgtttgtgttttagttttctgagagaaaattgcttgaaacttttgttttggtgggctggtttctttgacagATATGCCTCAATTAGGGCAATTGAGACCAAGTCCCCTGTTGATGATCAGCAATGGCTCACATACTGGGTTTTGTATTCTATGATCACACTCTTCGAGCTC
                || ||   |  |    ||   |||   | |  | |    | | | |||| |  | | ||| || |    |||   | || |||||||||| ||  || | || || || || || ||  |||| ||||||||||||||||||||||||||||| ||||| ||  | ||||| || || ||||||
---------------gtaagttactccagcactttcttttgtatgtaataaatacatacttcttgca-ttctagttctgat----tggacacctttacagATATGCATCTGTTCGAGCGATAGAAACAAAATCTGCTGTAGATGATCAGCAATGGCTCACATACTGGGTGTTGTACTCGTTTATCACTCTATTTGAGCTC

upper sequence: Vv17s0000g05990.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G130548_T01 (Zea mays), 3'ss of exon 2
-catgtatgttctataatatgtggtttgaatgtttgtgttttagttttctgagagaaaattgcttgaaacttttgttttggtgggctggtt-tctttgacagATATGCCTCAATTAGGGCAATTGAGACCAAGTCCCCTGTTGATGATCAGCAATGGCTCACATACTGGGTTTTGTATTCTATGATCACACTCTTCGAGCTC
  | ||     |  |||  | |    | ||  | |      ||  | | |        || | ||    ||| ||||||       |||   | ||  |||| ||||||||  |||| |||||||| || || ||  |||| |||||||||||||||||||| ||||||||  |||| ||  | ||||| || |||||||||
gtaagttaacccactaaccttttagataaacatatagacactaactgtattccgtttgatgg-ttattgcttctgttttacctcattggccattttccacagGTATGCCTCTGTTAGAGCAATTGAAACAAAATCTGCTGTGGATGATCAGCAATGGCTCACGTACTGGGTGCTGTACTCATTTATCACTCTATTCGAGCTC

upper sequence: Vv17s0000g05990.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G047860_T02 (Zea mays), 3'ss of exon 2
--------catgtatgttctataatatgtggtttgaatgtttgt--gttttagttttctgagagaaaattgcttgaaacttttgtt--ttggtgggctggtttctttgacagATATGCCTCAATTAGGGCAATTGAGACCAAGTCCCCTGTTGATGATCAGCAATGGCTCACATACTGGGTTTTGTATTCTATGATCACACTCTTCGAGCTC
        ||  | |||| | ||||     || || | |||| |   | ||  |  | || ||| |   |  ||  |  | |      ||  ||   |||   ||||| ||||||||| ||  |||| || || ||||| ||    ||||| ||||||||||| |||||||| |||||||| ||||| ||  | |||||  | || ||||| 
gtaagtatcacctttgttgt-taattgacagtctgtaggttttttcctcttgatactttgtgagcagtattgttatatttctaaccactttctgttttggcacctttg-cagATATGCTTCTGTTAGAGCTATAGAGACAAAAAATCCTGTAGATGATCAGCAGTGGCTCACTTACTGGGTGTTGTACTCGTTTATCACTTTGTTTGAGCTA

upper sequence: Vv17s0000g05990.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM5G862101_T02 (Zea mays), 3'ss of exon 2
catgtatgttctataatatgt-ggtttgaatgtttgtgttttagttttctgagagaaaattgcttgaaacttttgttttggtgggctggtttctttgacagATATGCCTCAATTAGGGCAATTGAGACCAAGTCCCCTGTTGATGATCAGCAATGGCTCACATACTGGGTTTTGTATTCTATGATCACACTCTTCGAGCTC
| |||   |   ||||| | | | | |   ||||  || |     | | ||||    | |    |    ||  |  |||  ||   |||   ||||| ||||||||| ||  |||| ||||| ||||| ||    ||||| ||||||||||| |||||||| |||||||| ||||| ||  |  ||||  | || ||||| 
cttgtgactaaaataattttttgatgttgttgttgatgatgatactatgtgagcactattgttatatttctaatcattttctgttttggcaactttg-cagATATGCTTCTGTTAGAGCAATAGAGACAAAAAATCCTGTAGATGATCAGCAGTGGCTCACTTACTGGGTGTTGTACTCATTTGTCACTTTGTTTGAGCTA

upper sequence: Vv17s0000g05990.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G177237_T01 (Zea mays), 3'ss of exon 2
catgtatgttctataatatgt-ggtttgaatgtttgtgttttagttttctgagagaaaattgcttgaaacttttgttttggtgggctggtttctttgacagATATGCCTCAATTAGGGCAATTGAGACCAAGTCCCCTGTTGATGATCAGCAATGGCTCACATACTGGGTTTTGTATTCTATGATCACACTCTTCGAGCTC
|||||   |   || || ||| | | |   ||||  || |     | | ||||    | |  | |    ||  |  |||  ||   |||   ||||| ||||||||| ||  |||| || || ||||| ||    ||||| ||||||||||| |||||||| |||||||| ||||| ||  |  ||||  | || ||||| 
catgtgactaaaatgatttgttgatgttgttgttgatgatgacactatgtgagcactattgtcatatttctaatcattttctgttttggcaactttg-cagATATGCTTCTGTTAGAGCGATAGAGACAAAAAATCCTGTAGATGATCAGCAGTGGCTCACTTACTGGGTGTTGTACTCATTTGTCACTTTGTTTGAGCTA

upper sequence: Vv17s0000g05990.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA06G20570.2 (Glycine max), 3'ss of exon 1
catgtatgttctataatatgtggtttgaatgtttgtgttttag----ttttctgagagaaaattgcttgaaacttt-tgttttggtgggctggtttctttgacagATATGCCTCAATTAGGGCAATTGAGACCAAGTCCCCTGTTGATGATCAGCAATGGCTCACATACTGGGTTTTGTATTCTATGATCACACTCTTCGAGCTC
    | ||||   |  ||| | | | |   |||  |||||||     || | |||||  | |||| || |   ||| || |||  | |     |  ||    ||||||||||||| ||||||||||||||| |||||| ||||||||||| |||||||||||||| || |||||| | |||||  ||||||| ||||| || || 
ttaatttgtttgtttttattttgctggctcgtt-atgttttaagctattgtttgagaatagattgattcatggtttatgatttctttgaacaatgcct----cagATATGCCTCAGTTAGGGCAATTGAGAGCAAGTCTCCTGTTGATGACCAGCAATGGCTCACTTATTGGGTTCTCTATTCCTTGATCACCCTCTTTGAACTT

upper sequence: Vv17s0000g05990.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA05G01160.1 (Glycine max), 3'ss of exon 2
---------------------------catgtatgttctataatatgtggt-ttgaatgtttgtgttttagtt-ttctgagagaaaattgcttgaaacttttgttttggtgggctggtttctttgacagATATGCCTCAATTAGGGCAATTGAGACCAAGTCCCCTGTTGATGATCAGCAATGGCTCACATACTGGGTTTTGTATTCTATGATCACACTCTTCGAGCTC
                               ||    | | ||| |||  | |||||||||  | ||  | || |||         | |  || | | | ||| | |||      |  || |    ||||||||| ||||||||||||||||||| |||||| ||| ||||||||||||| |||||||| ||||||||| | || ||  ||||||| ||||| || || 
gtaagcaaaatcttgatcttcctcttttccttacacgc-acaatgtgttttgttgaatgttccttttgcatttattccattgttggactcattcatattattgatgtgggttttcgtgttttgcttcagATATGCTTCAATTAGGGCAATTGAGAGCAAGTCTCCTATTGATGATCAGCAGTGGCTCACTTACTGGGTTCTCTACTCCTTGATCACCCTCTTTGAACTT

upper sequence: Vv17s0000g05990.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA04G33880.1 (Glycine max), 3'ss of exon 2
catgtatgttctataatatgtggtttgaatgtttgtgttttagttttctgagagaa--aattgcttgaaacttttgttttggtgggct-ggtttctttgacagATATGCCTCAATTAGGGCAATTGAGACCAAGTCCCCTGTTGATGATCAGCAATGGCTCACATACTGGGTTTTGTATTCTATGATCACACTCTTCGAGCTC
  ||| |||| | || | ||  | ||     | ||||||    | || |  |||||  ||| | ||||  | |   || || |    | |  |  |    ||||||||||||  ||||||||||||||| |||||| ||||||||||| |||||||||||||| || |||||| | || ||  ||||||| ||||| || || 
--tgtttgtttt-tattttgctggttcttgttatgtgttaagctattgttggagaatgaatagattgattcatggtttgtgatttctttgaataatgcttcagATATGCCTCGGTTAGGGCAATTGAGAGCAAGTCTCCTGTTGATGACCAGCAATGGCTCACTTATTGGGTTCTCTACTCCTTGATCACCCTCTTTGAACTT

upper sequence: Vv17s0000g05990.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA17G10730.1 (Glycine max), 3'ss of exon 2
----------------------------------------catgtatgttctataatatgtggtttgaatgtttgtgttttagttttctgagaga--aaattgct-tga--aacttttgttttggtgg-gctggtttctttg-------acagATATGCCTCAATTAGGGCAATTGAGACCAAGTCCCCTGTTGATGATCAGCAATGGCTCACATACTGGGTTTTGTATTCTATGATCACACTCTTCGAGCTC
                                         |||| | || | |   ||||    |     ||| |    | ||  | ||||||   |||||  | |||   | || | ||||  ||  |  |||||   ||        ||||||||| ||||||||||| ||||||| |||||| ||  ||||||||||||| |||||||| ||||||||| | || ||  ||||||||||||| || || 
gtaagtgcaatcttaatcttcctcgtttccttacatacactatgtgt-ttttgttgaatgttccatctgcatttattccattgtcctgtgagaggtcaaattattgtgactgatttattttttattgatgtgggttttcgtgttgtgctgcagATATGCTTCAATTAGGGCGATTGAGAGCAAGTCTCCCATTGATGATCAGCAGTGGCTCACTTACTGGGTTCTCTACTCCTTGATCACACTCTTTGAACTT

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|34544790|gb|CF513022.1|CF513022
EST:     GCCTGTCGTTAGTCTTGCTTATCCTCT                         ATATGCCTCAATTAGGGCAATTGAGACCAAGTCCCCTGTTGATGATCAGCA
genomic: GCCTGTCGTTAGTCTTGCTTATCCTCTgtaagtgggg ... tctttgacagATATGCCTCAATTAGGGCAATTGAGACCAAGTCCCCTGTTGATGATCAGCA
EST: gi|351016143|gb|FQ435463.1|FQ435463
EST:     GCCTGTCGTTAGTCTTGCTTATCCTCT                         ATATGCCTCAATTAGGGCAATTGAGACCAAGTCCCCTGTTGATGATCAGCA
genomic: GCCTGTCGTTAGTCTTGCTTATCCTCTgtaagtgggg ... tctttgacagATATGCCTCAATTAGGGCAATTGAGACCAAGTCCCCTGTTGATGATCAGCA
EST: gi|349825153|gb|FQ415700.1|FQ415700
EST:     GCCTGTCGTTAGTCTTGCTTATCCTCT                         ATATGCCTCAATTAGGGCAATTGAGACCAAGTCCCCTGTTGATGATCAGCA
genomic: GCCTGTCGTTAGTCTTGCTTATCCTCTgtaagtgggg ... tctttgacagATATGCCTCAATTAGGGCAATTGAGACCAAGTCCCCTGTTGATGATCAGCA
EST: gi|32458365|gb|CD799539.1|CD799539
EST:     GTCGTTAGTCTTGCTTATCCTCT                         ATATGCCTCAATTAGGGCAATTGAGAGACCAAGTCCCCTGTTGATGATCAG
genomic: GTCGTTAGTCTTGCTTATCCTCTgtaagtgggg ... tctttgacagATATGCCTCAATTAGGGCAATT--GAGACCAAGTCCCCTGTTGATGATCAG
EST: gi|349824511|gb|FQ413178.1|FQ413178
EST:     GCCTGTCGTTAGTCTTGCTTATCCTCT                         ATATGCCTCAATTGGGGCAATTGAGACCAAGTCCCCTGTTGATGATCAGCA
genomic: GCCTGTCGTTAGTCTTGCTTATCCTCTgtaagtgggg ... tctttgacagATATGCCTCAATTAGGGCAATTGAGACCAAGTCCCCTGTTGATGATCAGCA
EST: gi|110696491|gb|EE072653.1|EE072653
EST:     GCCTGTCGTTAGTCTTGCTTATCCTCT                         ATATGCCTCAATTAGGGCAATTGAGACCAAGTCCCCTGTTGATGATCAGCA
genomic: GCCTGTCGTTAGTCTTGCTTATCCTCTgtaagtgggg ... tctttgacagATATGCCTCAATTAGGGCAATTGAGACCAAGTCCCCTGTTGATGATCAGCA
EST: gi|71875506|gb|DT024561.1|DT024561
EST:     GCCTGTCGTTAGTCTTGCTTATCCTCT                         ATATGCCTCAATTAGGGCAATTGAGACCAAGTCCCCTGTTGATGATCAGCA
genomic: GCCTGTCGTTAGTCTTGCTTATCCTCTgtaagtgggg ... tctttgacagATATGCCTCAATTAGGGCAATTGAGACCAAGTCCCCTGTTGATGATCAGCA
EST: gi|349825152|gb|FQ415699.1|FQ415699
EST:     GCCTGTCGTTAGTCTTGCTTATCCTCT                         ATATGCCTCAATTAGGGCAATTGAGACCAAGTCCCCTGTTGATGATCAGCA
genomic: GCCTGTCGTTAGTCTTGCTTATCCTCTgtaagtgggg ... tctttgacagATATGCCTCAATTAGGGCAATTGAGACCAAGTCCCCTGTTGATGATCAGCA
EST: gi|351020210|gb|FQ445817.1|FQ445817
EST:     GCCTGTCGTTAGTCTTGCTTATCCTCT                         ATATGCCTCAATTAGGGCAATTGAGACCAAGTCCCCTGTTGATGATCAGCA
genomic: GCCTGTCGTTAGTCTTGCTTATCCTCTgtaagtgggg ... tctttgacagATATGCCTCAATTAGGGCAATTGAGACCAAGTCCCCTGTTGATGATCAGCA
EST: gi|351018684|gb|FQ424791.1|FQ424791
EST:     GCCTGTCGTTAGTCTTGCTTATCCTCT                         ATATGCCTCAATTAGGGCAATTGAGACCAAGTCCCCTGTTGATGATCAGCA
genomic: GCCTGTCGTTAGTCTTGCTTATCCTCTgtaagtgggg ... tctttgacagATATGCCTCAATTAGGGCAATTGAGACCAAGTCCCCTGTTGATGATCAGCA
EST: gi|110424630|gb|EC990997.1|EC990997
EST:     GCCTGTCGTTAGTCTTGCTTATCCTCT                         ATATGCCTCAATTAGGGCAATTGAGACCAAGTCCCCTGTTGATGATCAGCA
genomic: GCCTGTCGTTAGTCTTGCTTATCCTCTgtaagtgggg ... tctttgacagATATGCCTCAATTAGGGCAATTGAGACCAAGTCCCCTGTTGATGATCAGCA
EST: gi|349829195|gb|FQ419727.1|FQ419727
EST:     GCCTGTCGTTAGTCTTGCTTATCCTCT                         ATATGCCTCAATTAGGGCAATTGAGACCAAGTCCCCTGTTGATGATCAGCA
genomic: GCCTGTCGTTAGTCTTGCTTATCCTCTgtaagtgggg ... tctttgacagATATGCCTCAATTAGGGCAATTGAGACCAAGTCCCCTGTTGATGATCAGCA
EST: gi|294966237|gb|GW839460.1|GW839460
EST:     GCCTGTCGTTAGTCTTGCTTATCCTCT                         ATATGCCTCAATTAGGGCAATTGAGACCAAGTCCCCTGTTGATGATCAGCA
genomic: GCCTGTCGTTAGTCTTGCTTATCCTCTgtaagtgggg ... tctttgacagATATGCCTCAATTAGGGCAATTGAGACCAAGTCCCCTGTTGATGATCAGCA
EST: gi|34549707|gb|CF517939.1|CF517939
EST:     GCCTGTCGTTAGTCTTGCTTATCCTCT                         ATATGCCTCAATTAGGGCAATTGAGACCAAGTCCCCTGTTGATGATCAGCA
genomic: GCCTGTCGTTAGTCTTGCTTATCCTCTgtaagtgggg ... tctttgacagATATGCCTCAATTAGGGCAATTGAGACCAAGTCCCCTGTTGATGATCAGCA
EST: gi|110412973|gb|EC978742.1|EC978742
EST:     GCCTGTCGTTAGTCTTGCTTATCCTCT                         ATATGCCTCAATTAGGGCAATTGAGACCAAGTCCCCTGTTGATGATCAGCA
genomic: GCCTGTCGTTAGTCTTGCTTATCCTCTgtaagtgggg ... tctttgacagATATGCCTCAATTAGGGCAATTGAGACCAAGTCCCCTGTTGATGATCAGCA
EST: gi|349817530|gb|FQ407320.1|FQ407320
EST:     GCCTGTCGTTAGTCTTGCTTATCCTCT                         ATATGCCTCAATTAGGGCAATTGAGACCAAGTCCCCTGTTGATGATCGGCA
genomic: GCCTGTCGTTAGTCTTGCTTATCCTCTgtaagtgggg ... tctttgacagATATGCCTCAATTAGGGCAATTGAGACCAAGTCCCCTGTTGATGATCAGCA
EST: gi|110702147|gb|EE080527.1|EE080527
EST:     GCCTGTCGTTAGTCTTGCTTATCCTCT                         ATATGCCTCAATTAGGGCAATTGAGACCAAGTCCCCTGTTGATGATCAGCA
genomic: GCCTGTCGTTAGTCTTGCTTATCCTCTgtaagtgggg ... tctttgacagATATGCCTCAATTAGGGCAATTGAGACCAAGTCCCCTGTTGATGATCAGCA
EST: gi|349833130|gb|FQ416508.1|FQ416508
EST:     GCCTGTCGTTAGTCTTGCTTATCCTCT                         ATATGCCTCAATTAGGGCAATTGAGACCAAGTCCCCTGTTGATGATCAGCA
genomic: GCCTGTCGTTAGTCTTGCTTATCCTCTgtaagtgggg ... tctttgacagATATGCCTCAATTAGGGCAATTGAGACCAAGTCCCCTGTTGATGATCAGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctgagagaaaattgcttgaaacttttgttttggtgggctggtttctttgacagATATGCCTCAATTAGGGCAATTGAGACCAAGTCCCCTGTTGATGATCAGCAATGGCTCACATACTGGGTTTTGTATTCTATGATCACACTCTTCGAGCTC
                                           tttcttt  CT-rich tract
                        ttttgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catgtatgttctataatatgtggtttgaatgtttgtgttttagttttctgagagaaaattgcttgaaacttttgttttggtgggctggtttctttgacagATATGCCTCAATTAGGGCAATTGAGACCAAGTCCCCTGTTGATGATCAGCAATGGCTCACATACTGGGTTTTGTATTCTATGATCACACTCTTCGAGCTC

catgtat
- - - - - - - - - - tggtttg
- - - - - - - - - - - - - - - - - - - - - - - - - - agaaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcttga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gggctgg