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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtcagagttatattattataatgtatctgtacattgcaaatttgatgtttgaattatagatctattgcaacagaacatgaatttgattgttcattctcacagGTTCATTTTTTCCGTCCAGTTCCAAAAGAGTATTTGCATTCTGCTGAACTAAGAGATATAATGCAATTTGGTAGCAGCAATACTGCTGTATTTTTTAAGA

Basic information

species Vitis vinifera
transcript Vv04s0044g02020.t01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0044g02020.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: LOC_Os04g57140.1 (Oryza sativa), 3'ss of exon 9
gtgagtcagagttatattattataatgtatctgtacattgcaaatttgatgtttgaat--tatagatctattgcaacagaacatgaatttgattgtt--cattctcacagGTTCATTTTTTCCGTCCAGTTCCAAAAGAGTATTTGCATTCTGCTGAACTAAGAGATATAATGCAATTTGGTAGCAGCAATACTGCTGTATTTTTTAAGA
                             ||||   ||  | ||    |||||  |||  ||||  | |  ||| |         |||||  || |   | ||    |||||||||||||||||||| ||||| || || ||| | |||||||| ||||| |||||||| ||||||||||| ||||||||||| ||||| || ||||| |
----------------------------gtctg---atgcctaaccacatgttgaaatgctatacgttttctgccagttttagctaatttctttttctgcgttaatgcagGTTCATTTTTTCCGTCCGGTTCCCAAGGAATATCTTCATTCTGCAGAACTGAGAGATATCATGCAATTTGGGAGCAGCAATACCGCTGTTTTCTTTAAAA

upper sequence: Vv04s0044g02020.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GRMZM2G423861_T01 (Zea mays), 3'ss of exon 10
gtgagtcagagttatattattataatgtatctgtacattgcaaatttgatgtttgaattatagatctattgcaacagaacatgaatttgattgttcattctcacagGTTCATTTTTTCCGTCCAGTTCCAAAAGAGTATTTGCATTCTGCTGAACTAAGAGATATAATGCAATTTGGTAGCAGCAATACTGCTGTATTTTTTAAGA
                    | | || |  |  | |  || ||| || || ||     | |   |  | |  ||| || | |||||||     | |||     |||||||| ||||||||||||||||| || || ||| | |||||||| ||| ||||||| || ||||||||||||||||||||||||||||| || ||||| |
-------------------gtctgatctcaccatgcgatggaaacttcatattc----tttctgttaagtaaaactgatcttgaattta----tgcatgaatgcagGTTCACTTTTTCCGTCCAGTTCCCAAGGAATATCTTCATTCTGCAGAATTAAGAGACATCATGCAATTTGGTAGCAGCAATACTGCTGTTTTCTTTAAAA

upper sequence: Vv04s0044g02020.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GRMZM2G070273_T01 (Zea mays), 3'ss of exon 9
gtgagtcagagttatattattataatgtatctgtacattgcaaatttgatgtttgaattatagatctattgcaacagaacatgaatttgattgttcattctcacagGTTCATTTTTTCCGTCCAGTTCCAAAAGAGTATTTGCATTCTGCTGAACTAAGAGATATAATGCAATTTGGTAGCAGCAATACTGCTGTATTTTTTAAGA
                   |   |      |  |  | || ||  || || ||     | |      | |  ||| || | |||||||     | |||     |||||||| |||||||| || ||||| || || ||| | |||||||| ||||||||||| || ||||||||||||||||||||||||||||| || ||||| |
------------------gtctgatctcgaccatgtaatggaagcttcatattc----tttctgctaagtaaaactgaccttgaatttc----tgcatgaatgcagGTTCACTTTTTCCGCCCGGTTCCCAAGGAATATCTTCATTCTGCAGAACTAAGAGACATCATGCAATTTGGTAGCAGCAATACTGCTGTCTTCTTTAAAA

upper sequence: Vv04s0044g02020.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA11G09480.1 (Glycine max), 3'ss of exon 11
gtgagtcagagttatattattataatgt---atctgtacattgcaaatttgatgtttgaattatagatcta-ttgcaacagaacatgaatttgattgttcattctcacagGTTCATTTTTTCCGTCCAGTTCCAAAAGAGTATTTGCATTCTGCTGAACTAAGAGATATAATGCAATTTGGTAGCAGCAATACTGCTGTATTTTTTAAGA
    || ||| | | || |||  ||| |      | ||   |  ||| ||  | ||| ||    |  | |  ||  ||  |||  |   ||| ||   | |||| ||  ||| |||||||||||||| |||||||| || ||| |||| ||||||||| | ||||| |||||||||||||| |||||||||||||| ||||||||||| |
----gtaagactaacatgatttaaattttaagattataaggtttaaaatttctttttaaaaacgaattgtgcttttaattgaatgtttttttaataaattattccca--gGTCCATTTTTTCCGTCCCGTTCCAAAGGAATATATGCACTCTGCTGAATTGAGAGACATAATGCAATTTGGAAGCAGCAATACTGCAGTATTTTTTAAAA

upper sequence: Vv04s0044g02020.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA16G21340.1 (Glycine max), 3'ss of exon 14
gtgagtcagagttatattatta-taatgtatctgtacattgca-aatttgatgtttgaattatagatctat------tgcaacagaacatgaatttgattgttcattc--tcacagGTTCATTTTTTCCGTCCAGTTCCAAAAGAGTATTTGCATTCTGCTGAACTAAGAGATATAATGCAATTTGGTAGCAGCAATACTGCTGTATTTTTTAAGA
||  | |  |   | |  || | || |  | ||  |||||  | | |||  | ||  ||||||  |   ||      |||     |   ||  |||  ||| ||| |     | || |||||||||||||||||||||| || || |||||||| || |||||  | ||||| |||||||||||||| |||||||||||||| || |||||||| |
gtatgactaaacaaaaaaataactagttaaactaaacattatatagtttactattacaattattaaaaaatgaactgtgcttttaattgtgttttttcttgatcaattggctatagATTCATTTTTTCCGTCCAGTTCCTAAGGAATATTTGCACTCAGCTGAGTTGAGAGACATAATGCAATTTGGAAGCAGCAATACTGCAGTCTTTTTTAAAA

upper sequence: Vv04s0044g02020.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA01G35950.1 (Glycine max), 3'ss of exon 11
gtgagtcagagttatattattataat-gtatctgtacattgcaaa-tttgatgtttgaattatagatctattgcaacagaacatgaatttgattgttcattctcacagGTTCATTTTTTCCGTCCAGTTCCAAAAGAGTATTTGCATTCTGCTGAACTAAGAGATATAATGCAATTTGGTAGCAGCAATACTGCTGTATTTTTTAAGA
          || ||| ||  || ||   || |  ||| |  ||  ||| |   ||   ||  | | ||| |      |||  |   ||  ||   | |||| ||  ||| ||||||||||||||  ||||||| || ||| |||| ||||||||  | || || |||||||||||||| |||||||||||||| ||||||||||| |
----------gtaatactaacatgattaaattttaacactataaggtttaaaacttctttttaaaaactaat-tgtttgaattttttttcaataaattattccca--gGTCCATTTTTTCCGTCCCATTCCAAAGGAATATATGCACTCTGCTGAGTTGAGGGACATAATGCAATTTGGAAGCAGCAATACTGCAGTATTTTTTAAAA

upper sequence: Vv04s0044g02020.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA09G32740.1 (Glycine max), 3'ss of exon 11
------gtgagtcagagttatattattataatgtatctgtacattgcaaatttgatgtttgaattatagatctattgcaacagaacatgaatttgattg-ttcattc-tcacagGTTCATTTTTTCCGTCCAGTTCCAAAAGAGTATTTGCATTCTGCTGAACTAAGAGATATAATGCAATTTGGTAGCAGCAATACTGCTGTATTTTTTAAGA
       | | | | |      |||   |||    | | ||  ||   | |   ||  || ||  ||  ||          |     ||  |||  ||| | ||||    | || |||||||||||||||||||||| || || |||||||| || |||||  | ||||| |||||||||||||| ||||| |||||||| || || ||||| |
gtatgactaaatgaaaaactagttaaactaaacattatatagtttatcattacaattattaaagaatgaattgtgcttttaattgtgtgccttttcttgatccattggctatagATTCATTTTTTCCGTCCAGTTCCTAAGGAATATTTGCACTCAGCTGAGTTGAGAGACATAATGCAATTTGGAAGCAGTAATACTGCAGTCTTCTTTAAAA

upper sequence: Vv04s0044g02020.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: AT5G65930.1 (Arabidopsis thaliana), 3'ss of exon 8
gtgagtcagagttatattattataatgtatctgtacattgcaaat----ttgatgtttgaattatagatctattgcaacagaacatgaatttgattgtt-cattctcacagGTTCATTTTTTCCGTCCAGTTCCAAAAGAGTATTTGCATTCTGCTGAACTAAGAGATATAATGCAATTTGGTAGCAGCAATACTGCTGTATTTTTTAAGA
|| ||||  | |   | | |||||   |||   |  |    || |    ||| |||||| | |  | |||||| |     | |  |||||||| |  || | ||||   ||||||| ||||| || || ||||| ||||| ||| |||| |||||||||||| | || || ||||||||||| ||||| || |||||||| ||||| || |
gttagtctcaatataaatgttatacattatgactttaaaaaaactgttattgttgtttggaattcaaatctat-gttgttggatttgaatttgttgtttgctttcttgtagGTTCACTTTTTTCGACCGGTTCCTAAAGAATATCTGCACTCTGCTGAACTACGTGACATCATGCAATTTGGCAGCAGTAACACTGCTGTCTTTTTCAAAA

upper sequence: Vv04s0044g02020.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: PP1S364_50V6.1 (Physcomitrella patens), 3'ss of exon 12
------------------------------------------------------gtgagt--cagagttatattattataatgt-atctgt-acattgcaaatttgatgtt--tgaattatagatctattg-caacagaacatgaatttgattgttcat-------tctcacagGTTCATTTTTTCCGTCCAGTTCCAAAAGAGTATTTGCATTCTGCTGAACTAAGAGATATAATGCAATTTGGTAGCAGCAATACTGCTGTATTTTTTAAGA
                                                       |||    | | ||| |     | |    | || ||| |  |    | ||||||  |  ||   |||||   | ||| |       | || ||||  ||  |||        | |  ||||| ||||||||||| || || || ||||||||||||||||| ||||||||  | || || |||||||||||||||||||| || || || ||||| || |
gtatgtgggagcgccttcatctttgtatgctttatcacttccataaacatttttatgaccagctgcgttgtgacgcttttccctcatatgttatttcatgactttgattatcgtggggtatagggtttttgacgttgttgcctgcatttattttgtcacgtttctgtattgcagGTGCATTTTTTCCGACCTGTGCCTAAAGAGTATTTGCATTCAGCTGAACTGCGCGACATTATGCAATTTGGTAGCAGCAACACAGCCGTCTTTTTCAAAA

upper sequence: Vv04s0044g02020.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: EFJ30174 (Selaginella moellendorffii), 3'ss of exon 10
gtgagtcagagttatattattataatgtatctgtacattgcaaatttgatgtttgaattatagatctattgcaacagaacatgaatttgat-tgttcattctcacagGTTCATTTTTTCCGTCCAGTTCCAAAAGAGTATTTGCATTCTGCTGAACTAAGAGATATAATGCAATTTGGTAGCAGCAATACTGCTGTATTTTTTAAGA
                                                       |  |  |  | |||| ||   |  |     |||||  |||   |  | |||||||||||||||||| ||||| || ||||| ||||| ||||| ||||| || ||||| || ||||||||||| || |||||||| || || |||||||| |
-----------------------------------------------------gtacgtgcaagtatatt-ca--tgttcgctgttttgacatgtgtttcttaacagGTTCATTTTTTCCGGCCAGTACCTAAAGAATATTTACATTCGGCTGAGCTGAGAGACATCATGCAATTTGGAAGTAGCAATACCGCAGTGTTTTTTAAAA

upper sequence: Vv04s0044g02020.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: EFJ06058 (Selaginella moellendorffii), 3'ss of exon 10
gtgagtcagagttatattattataatgtatctgtacattgcaaatttgatgtttgaattatagatctattgcaacagaacatgaatttgat-tgttcattctcacagGTTCATTTTTTCCGTCCAGTTCCAAAAGAGTATTTGCATTCTGCTGAACTAAGAGATATAATGCAATTTGGTAGCAGCAATACTGCTGTATTTTTTAAGA
                                                       |  |  |  | |||| ||   |  |  |  |||||  |||   |  | |||||||||||||||||| ||||| || ||||| ||||| ||||| ||||| || ||||| || ||||||||||| || |||||||| || || |||||||| |
-----------------------------------------------------gtacgtgcaagtatatt-ca--tgttcgcggttttgacatgtgtttcttaacagGTTCATTTTTTCCGGCCAGTACCTAAAGAATATTTACATTCGGCTGAGCTTAGAGACATCATGCAATTTGGAAGTAGCAATACCGCAGTGTTTTTTAAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgaattatagatctattgcaacagaacatgaatttgattgttcattctcacagGTTCATTTTTTCCGTCCAGTTCCAAAAGAGTATTTGCATTCTGCTGAACTAAGAGATATAATGCAATTTGGTAGCAGCAATACTGCTGTATTTTTTAAGA
                                 atttgat  putative branch site (score: 5)
                                          ttcattctc  putative PPT
     attatagatctatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtcagagttatattattataatgtatctgtacattgcaaatttgatgtttgaattatagatctattgcaacagaacatgaatttgattgttcattctcacagGTTCATTTTTTCCGTCCAGTTCCAAAAGAGTATTTGCATTCTGCTGAACTAAGAGATATAATGCAATTTGGTAGCAGCAATACTGCTGTATTTTTTAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA