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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgttcaggcacacagatttaatagttattgatgaatcccattgcctatgctcattttttttttttttttttaatgtgaattccagGAATCACAATCGCTGAATATTTTAGAGATATGGGCTACAATGTTAGTATGATGGCAGACTCAACTTCCCGTTGGGCAGAAGCATTAAGAGAAATTTCAGG

Basic information

species Arabidopsis thaliana
transcript AT1G78900.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G78900.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: LOC_Os06g45120.1 (Oryza sativa), 3'ss of exon 11
----------gtaatgttc--aggcacacagatttaatagttattgatgaatcccattgcctatgctcattttttttttttttttttaatgtgaattccagGAATCACAATCGCTGAATATTTTAGAGATATGGGCTACAATGTTAGTATGATGGCAGACTCAACTTCCCGTTGGGCAGAAGCATTAAGAGAAATTTCAGG
            ||   |   |||    |    ||| |  |  || |||  |    ||  || |    |        |  | |||||  | ||    |||||||| ||||| |||||||| ||  | || |||||||| ||||| ||||||||||| || || ||||| || ||||| ||||| ||  | || ||||||||
agtttcttgtagaacactaaaaggagtccttgcttagttatgctttatgcctgatgttttctttatcaacaaaacaatcatatttttt-tctgcccaccagGAATTACAATTGCTGAATACTTCCGTGACATGGGCTATAATGTCAGTATGATGGCTGATTCTACTTCTCGGTGGGCTGAAGCTTTGCGTGAGATTTCAGG

upper sequence: AT1G78900.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GRMZM2G128877_T03 (Zea mays), 3'ss of exon 8
gtaatgttcaggcacacagatttaatagttattgatgaatcccattgcctatgctc-------attttttttttttttttttaatgtgaattc------cagGAATCACAATCGCTGAATATTTTAGAGATATGGGCTACAATGTTAGTATGATGGCAGACTCAACTTCCCGTTGGGCAGAAGCATTAAGAGAAATTTCAGG
 | || |   ||  |     |  |   || | |  |   ||   ||| |  || ||       | ||| | ||     |  || |||   ||       ||||||| ||||| || || |||||| | |||||||||||||| |||||||||||||| ||||| || || || ||||| || || ||  | || || |||||
atgatat--gggtgcctctgtccatctgtcagttgtatctctgcttgtcgctgttcggtgtggagtttctgttaacaatcatattgtacctttttcccgcagGAATTACAATTGCCGAGTATTTTCGTGATATGGGCTACAACGTTAGTATGATGGCTGACTCCACCTCACGATGGGCTGAGGCTTTGCGTGAGATCTCAGG

upper sequence: AT1G78900.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GRMZM2G421857_T02 (Zea mays), 3'ss of exon 11
----------gtaatgttcaggcacacagatttaatagttattgatgaatcccattgccta-tgctcattttttttttttttttttaatgtgaattccagGAATCACAATCGCTGAATATTTTAGAGATATGGGCTACAATGTTAGTATGATGGCAGACTCAACTTCCCGTTGGGCAGAAGCATTAAGAGAAATTTCAGG
          |     |||||     ||| | || |  |  |||  |  |  || |||  | |     ||     |  | || |    | |  |   ||||||| ||||| ||||| |||||  | |||||||||||||| || ||||||||||| ||||| || ||||| ||||| || |||||  | || || |||||
tgatatgggtgcctctttcagtttgtcagctgtatttctgcttgtcgcttttcagtgcagagtttctgttaacaatcatgttgtaccttttttaactcagGAATTACAATTGCTGAGTATTTCCGTGATATGGGCTACAACGTCAGTATGATGGCTGACTCCACCTCCCGGTGGGCTGAGGCATTGCGTGAGATCTCAGG

upper sequence: AT1G78900.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA07G00430.1 (Glycine max), 3'ss of exon 12
----------gtaatgttcaggcacacagatttaat-agttattgatgaatcccattgcctatgctcattttttttttttttttttaatgtgaattccagGAATCACAATCGCTGAATATTTTAGAGATATGGGCTACAATGTTAGTATGATGGCAGACTCAACTTCCCGTTGGGCAGAAGCATTAAGAGAAATTTCAGG
              | |   |    | | ||||  |  |    || || ||   | |    |  || |||||  |  | |  || |  | |||||| ||||||||||| | ||||| ||||||||||||||||| || ||||| |||||||||||||| || || ||  | ||||||||||||||  | ||||| || ||
atcatattttcccttataatgattaataaatttgtttggcctgtgctgcatgagagttttaacactgattttgataatgtaattcttttttgaattgcagGAATCACATTAGCTGAGTATTTTAGAGATATGGGTTATAATGTCAGTATGATGGCAGATTCTACATCTAGATGGGCAGAAGCATTGCGTGAAATCTCTGG

upper sequence: AT1G78900.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA08G23990.1 (Glycine max), 3'ss of exon 12
-------------gtaatgttcaggcacacagatttaata---gttattgatgaatcccattgcctatgctcattttttttttttttttttaatgtgaattccagGAATCACAATCGCTGAATATTTTAGAGATATGGGCTACAATGTTAGTATGATGGCAGACTCAACTTCCCGTTGGGCAGAAGCATTAAGAGAAATTTCAGG
               |||| | |   | |  | || |      | |  |   || |   |   |  ||  | ||  | | ||| |||||||    | |||| ||||||||||| | ||||| ||||| ||||||||||| || ||||| |||||||||||||| || || ||  | ||||||||||||||  | ||||| || ||
tatatttgcccttaaaatgattaatga-attgtttgaccgtgtgctgcttgagagttttaacactgattttgataatatatttcttttttt----tcaattgcagGAATCACATTAGCTGAGTATTTCAGAGATATGGGTTATAATGTCAGTATGATGGCAGATTCTACATCTAGATGGGCAGAAGCATTGCGTGAAATCTCTGG

upper sequence: AT1G78900.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: Vv04s0008g02580.t01 (Vitis vinifera), 3'ss of exon 12
------------gtaatgttcaggcacacagatttaatagttattgatgaatcccattgcctatgctcattttttttttttttttt-taatgtgaattccagGAATCACAATCGCTGAATATTTTAGAGATATGGGCTACAATGTTAGTATGATGGCAGACTCAACTTCCCGTTGGGCAGAAGCATTAAGAGAAATTTCAGG
            |   | ||  ||   |   |  |  |    | |  || ||    ||    |   | ||||| |       | |  | |||  |  | |||| |||||||| || ||||| |||||||| ||||| |||||||| |||||||||||||| ||||| || |||||||| || || ||  | || || || ||
tttccattggtagcttttttttggtgaagcaacatttttccaagttttgtatat--ttattcaaaattattttctaaaccaatgtgatcatggaatgttcagGTATCACAATTGCCGAATACTTTAGAGACATGGGTTACAATGTCAGTATGATGGCAGATTCAACATCTCGTTGGGCTGAGGCTTTGCGTGAGATATCTGG

upper sequence: AT1G78900.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: Vv09s0054g00890.t01 (Vitis vinifera), 3'ss of exon 12
----------gtaatgttcaggcacacagatttaatagttattgatgaatcccattgcctatgctcattttttttttttttttttaatgtgaattc--cagGAATCACAATCGCTGAATATTTTAGAGATATGGGCTACAATGTTAGTATGATGGCAGACTCAACTTCCCGTTGGGCAGAAGCATTAAGAGAAATTTCAGG
           || || ||  |   |     ||  |  |   |  | |       ||| |  | | || || |     |  | | | ||||  ||   |||| ||||| || |||||||| || ||||||||||||||||||||||||||||||||||| ||||| || || |||||||| |||||  ||||||| |||||
cctgaagcttttagtggtcttgtctatcacctttgtgttaccttgttatggaaggtgc-tgagatgatgttctccaactaatatgattgtgggtttttcagGTATCACTATAGCTGAATACTTCAGAGATATGGGCTACAATGTTAGTATGATGGCAGATTCAACATCTCGATGGGCAGAGGCATTGCGAGAAATATCAGG

upper sequence: AT1G78900.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: PP1S10_201V6.1 (Physcomitrella patens), 3'ss of exon 12
-------------gtaatgttcaggcacacagatttaatagttat-tga---tgaatcccattgcctatgctcatttttttttttttt--ttttaatgtgaattccagGAATCACAATCGCTGAATATTTTAGAGATATGGGCTACAATGTTAGTATGATGGCAGACTCAACTTCCCGTTGGGCAGAAGCATTAAGAGAAATTTCAGG
             || ||  | | ||  | |  ||| || |  || |||   | ||         ||      |||||   ||  |    ||||  | |   || |||| || ||  | || || || || || |||||||| || ||||| ||||||||||| |||||||| || || |||||||| ||  | ||||||||||| ||
gttcccatcttgagttattctgaagctta-acttttgatcgcaatgtgaccttaaagtttgaaatcttgaaggattttacgttcatcacattttgttatctgttgcagGTATTACCTTGGCGGAGTACTTCAGGGATATGGGGTATAATGTCAGTATGATGGCGGACTCAACATCTCGCTGGGCAGAGGCTCTTAGAGAAATTTCCGG

upper sequence: AT1G78900.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: PP1S8_312V6.1 (Physcomitrella patens), 3'ss of exon 12
-----------------------------------gtaatgttcaggcaca---cagatttaatagttattgatgaatcccattgcctatgctcatttttttt----ttttttttttaatgtgaattcc------agGAATCACAATCGCTGAATATTTTAGAGATATGGGCTACAATGTTAGTATGATGGCAGACTCAACTTCCCGTTGGGCAGAAGCATTAAGAGAAATTTCAGG
                                   ||  |||       ||   ||   |   | | | ||    ||| | ||    |||| ||   |  ||     |  || |   ||||    ||||      ||| |||||  | || ||||| || || |||||||| |||||||| ||||||||||||||||| || || || ||||| || ||  |  | || ||||| ||
gttattttcttttcttctgagactctactttctaggtgctgtatgaaaccatttcatcctctttggatgtttg-aaatgctatcctgtatgatcgcatacttccgcatcattatgcaaatgctgtttcctgttgcagGTATCACTTTGGCAGAATACTTCAGGGATATGGGTTACAATGTCAGTATGATGGCAGACTCTACATCTCGCTGGGCTGAGGCGCTTCGTGAGATTTCTGG

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|125318817|gb|EL332902.1|EL332902
EST:     CTCTAACATGCCTGTGGCTGCTCGTGAAGCCTCAATTTACACAG                         GAATCACAATCGCTGAATATTTTAGAGATATGGGCTACAATGTTAGTA
genomic: CTCTAACATGCCTGTGGCTGCTCGTGAAGCCTCAATTTACACAGgtaatgttca ... tgaattccagGAATCACAATCGCTGAATATTTTAGAGATATGGGCTACAATGTTAGTA
EST: gi|116463760|gb|EG506352.1|EG506352
EST:     TAACACCTCTAACATGCCTGTGGCTGCTCGTGAAGCCTCAATTTACACAG                         GAATCACAATCGCTGAATATTTTAGAGATATGGGCTACAATGTTAGTATGA
genomic: TAACACCTCTAACATGCCTGTGGCTGCTCGTGAAGCCTCAATTTACACAGgtaatgttca ... tgaattccagGAATCACAATCGCTGAATATTTTAGAGATATGGGCTACAATGTTAGTATGA
EST: gi|116463788|gb|EG506380.1|EG506380
EST:     TAACACCTCTAACATGCCTGTGGCTGCTCGTGAAGCCTCAATTTACACAG                         GAATCACAATCGCTGAATATTTTAGAGATATGGGCTACAATGTTAGTATGA
genomic: TAACACCTCTAACATGCCTGTGGCTGCTCGTGAAGCCTCAATTTACACAGgtaatgttca ... tgaattccagGAATCACAATCGCTGAATATTTTAGAGATATGGGCTACAATGTTAGTATGA
EST: gi|125096720|gb|EL153421.1|EL153421
EST:     TAACACCTCTAACATGCCTGTGGCTGCTCGTGAAGCCTCAATTTACACAG                         GAATCACAATCGCTGAATA
genomic: TAACACCTCTAACATGCCTGTGGCTGCTCGTGAAGCCTCAATTTACACAGgtaatgttca ... tgaattccagGAATCACAATCGCTGAATA
EST: gi|124918837|gb|EH992638.1|EH992638
EST:     ACCTCTAACATGCCTGTGGCTGCTCGTGAAGCCTCAATTTACACAG                         GAATCACAATCGCTGAATATTTTAGAGATATGGGCTACAATGTTAGTA
genomic: ACCTCTAACATGCCTGTGGCTGCTCGTGAAGCCTCAATTTACACAGgtaatgttca ... tgaattccagGAATCACAATCGCTGAATATTTTAGAGATATGGGCTACAATGTTAGTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgaatcccattgcctatgctcattttttttttttttttttaatgtgaattccagGAATCACAATCGCTGAATATTTTAGAGATATGGGCTACAATGTTAGTATGATGGCAGACTCAACTTCCCGTTGGGCAGAAGCATTAAGAGAAATTTCAGG
                                     ttttaat  putative branch site (score: 3)
                   ctcatttttttttttt  CT-rich tract
               tatgctcatttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatgttcaggcacacagatttaatagttattgatgaatcccattgcctatgctcattttttttttttttttttaatgtgaattccagGAATCACAATCGCTGAATATTTTAGAGATATGGGCTACAATGTTAGTATGATGGCAGACTCAACTTCCCGTTGGGCAGAAGCATTAAGAGAAATTTCAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA