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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taatggtttgtatgataacacaaatgtgaaaagtagaatagaatgccatgtatttggaagcagagtggattggaactaattgtatatttttatattccagAGATCGAGCTGGGGGCTACACAAGAATGTTAAGAACCAGGATACGTGTTGGTGATGCTGCTCCAATGGCATACATCGA

Basic information

species Zea mays
transcript GRMZM2G112865_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G112865_T03 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g62210.1 (Oryza sativa), 3'ss of exon 4
---taatggtttgtatgataacacaaatgtgaaa-agtagaatagaatgccatgtatttggaagcagagtggattggaactaattgtatatttttatattccagAGATCGAGCTGGGGGCTACACAAGAATGTTAAGAACCAGGATACGTGTTGGTGATGCTGCTCCAATGGCATACATCGA
    |     |||||  |  | |    | || |   |||| ||||  |   |  |||||  | |  ||    | ||   ||   | | |   |||  | |  ||  | |||||||| || ||||| ||| | ||  |||| |||||||| |||||||||||||| || ||||||||||| ||
catcacaaaattgtaatactagaacgctatgtactggtagcatagggtcata-atatttttaggtcgatcctaatgattct---tttgtcccttttgaatttagGAACCGAGCTGGTGGGTACACCAGACTATTGCGAACTAGGATACGAGTTGGTGATGCTGCACCGATGGCATACATTGA

upper sequence: GRMZM2G112865_T03 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os05g38580.1 (Oryza sativa), 3'ss of exon 4
--------------------------taatggtttgtatgataacacaaatg-tgaaaagta-gaatagaatgccatgtatttggaagcagagtggattggaactaattgtatatttttatattccagAGATCGAGCTGGGGGCTACACAAGAATGTTAAGAACCAGGATACGTGTTGGTGATGCTGCTCCAATGGCATACATCGA
                          |     |||  ||  | |      |  ||   || | |  || |    | ||  | |  |     |    ||        ||| | | |  ||   ||  |||||||||||||| || || |||||| |  |  | || |||||||| ||||| |||||||| |||||||||||||| ||
gtaacttttagcccgctatgagttggtttcacttttgattttgatttttgttctggctagcatgtctaaaggaacttggctgtcaagatttaccttatgcatgtccattatgtttcctttgtttgtagAGATCGAGCTGGTGGATATACAAGACTACTGCGGACTAGGATACGGGTTGGCGATGCTGCACCAATGGCATACATTGA

upper sequence: GRMZM2G112865_T03 (Zea mays), 3'ss of exon 3
lower sequence: AT5G09770.1 (Arabidopsis thaliana), 3'ss of exon 4
taatggtttgtatgataacacaaatgtgaaaagtagaatagaatgccatgtatttggaagcagagtggattggaactaattgtatatttttatattccagAGATCGAGCTGGGGGCTACACAAGAATGTTAAGAACCAGGATACGTGTTGGTGATGCTGCTCCAATGGCATACATCGA
     ||  || |   ||  |   ||  |  | |  || ||    |||| |   |  ||||    || |||  | ||   | |||||| || | || ||||||| ||||||| || ||||||||| || || | ||  | ||||| ||||||||||||||||| ||||| || |||||
-----gtgagtcttcaaattcttttggcatcattttaacag---tccat-tgcct--aagcgctttgcatt--atctggatatatattatt-tgttacagAGATAGAGCTGGTGGATACACAAGACTGCTACGTACTCGCATACGAGTTGGTGATGCTGCTCCTATGGCCTATATCGA

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|32909297|gb|CF014109.1|CF014109
EST:     GGTGATGATGTCGTTCATAAGCTATTTACTGAGCTGGCCTTTCGCTACAG                         AGATCGAGCTGGGGGCTACACAAGAATGTTAAGAACCAGGATACGTGTTGG
genomic: GGTGATGATGTCGTTCATAAGCTATTTACTGAGCTGGCCTTTCGCTACAGgtaatctgtt ... tatattccagAGATCGAGCTGGGGGCTACACAAGAATGTTAAGAACCAGGATACGTGTTGG
EST: gi|50337604|gb|CO532730.1|CO532730
EST:     GGTGATGATGTCGTTCATAAGCTATTTACTGAGCTGGCCTTTCGCTACAG                         AGATCGAGCTGGGGGCTACACAAGAATGTTAAGAACCAGGATACGTGTTGG
genomic: GGTGATGATGTCGTTCATAAGCTATTTACTGAGCTGGCCTTTCGCTACAGgtaatctgtt ... tatattccagAGATCGAGCTGGGGGCTACACAAGAATGTTAAGAACCAGGATACGTGTTGG
EST: gi|110963515|gb|EE183415.1|EE183415
EST:     GGTGATGATGTCGTTCATAAGCTATTTACTGAGCTGGCCTTTCGCTACAG                         AGATCGAGCTGGGGGCTACACAAGAATGTTAAGAACCAGGATACGTGTTGG
genomic: GGTGATGATGTCGTTCATAAGCTATTTACTGAGCTGGCCTTTCGCTACAGgtaatctgtt ... tatattccagAGATCGAGCTGGGGGCTACACAAGAATGTTAAGAACCAGGATACGTGTTGG
EST: gi|33099991|gb|CF059951.1|CF059951
EST:     GGTGATGATGTCGTTCATAAGCTATTTACTGAGCTGGCCTTTCGCTACAG                         AGATCGAGCTGGGGGCTACACAAGAATGTTAAGAACCAGGATACGTGTTGG
genomic: GGTGATGATGTCGTTCATAAGCTATTTACTGAGCTGGCCTTTCGCTACAGgtaatctgtt ... tatattccagAGATCGAGCTGGGGGCTACACAAGAATGTTAAGAACCAGGATACGTGTTGG
EST: gi|37393499|gb|CF634015.1|CF634015
EST:     GGTGATGATGTCGTTCATAAGCTATTTACTGAGCTGGCCTTCCGCTACAG                         AGATCGAGCTGGGGGCTACACAAGAATGTTAAGAACCAGGATACGTGTTGG
genomic: GGTGATGATGTCGTTCATAAGCTATTTACTGAGCTGGCCTTTCGCTACAGgtaatctgtt ... tatattccagAGATCGAGCTGGGGGCTACACAAGAATGTTAAGAACCAGGATACGTGTTGG
EST: gi|113684918|gb|DW837812.1|DW837812
EST:     GGTGATGATGTCGTTCATAAGCTATTTACTGAGCTGGCCTTTCGCTACAG                         AGATCGAGCTGGGGGCTAC
genomic: GGTGATGATGTCGTTCATAAGCTATTTACTGAGCTGGCCTTTCGCTACAGgtaatctgtt ... tatattccagAGATCGAGCTGGGGGCTAC
EST: gi|211500584|gb|FL212575.1|FL212575
EST:     GGTGATGATGTCGTTCATAAGCTATTTACTGAGCTGGCCTTTCGCTACAG                         AGATCGAGCTGGGGGCTACACAAGAATGTTAAGAACCAGGATACGTGTTGG
genomic: GGTGATGATGTCGTTCATAAGCTATTTACTGAGCTGGCCTTTCGCTACAGgtaatctgtt ... tatattccagAGATCGAGCTGGGGGCTACACAAGAATGTTAAGAACCAGGATACGTGTTGG
EST: gi|113740638|gb|DW856220.1|DW856220
EST:     GTGATGATGTCGTTCATAAGCTATTTACTGAGCTGGCCTTTCGCTAACAG                         AGATCGAGCTGGGGGCTAC
genomic: GTGATGATGTCGTTCATAAGCTATTTACTGAGCTGGCCTTTCGCTA-CAGgtaatctgtt ... tatattccagAGATCGAGCTGGGGGCTAC
EST: gi|60353121|gb|DN220094.1|DN220094
EST:     GGTGATGATGTCGTTCATAAGCTATTTACTGAGCTGGCCTTTCGCTACAG                         AGATCGAGCTGGGGGCTACACAAGAATGTTAAGAACCAGGATACGTGTTGG
genomic: GGTGATGATGTCGTTCATAAGCTATTTACTGAGCTGGCCTTTCGCTACAGgtaatctgtt ... tatattccagAGATCGAGCTGGGGGCTACACAAGAATGTTAAGAACCAGGATACGTGTTGG
EST: gi|60356193|gb|DN223166.1|DN223166
EST:     GGTGATGATGTCGTTCATAAGCTATTTACTGAGCTGGCCTTTCGCTACAG                         AGATCGAGCTGGGGGCTACACAAGAATGTTAAGAACCAGGATACGTGTTGG
genomic: GGTGATGATGTCGTTCATAAGCTATTTACTGAGCTGGCCTTTCGCTACAGgtaatctgtt ... tatattccagAGATCGAGCTGGGGGCTACACAAGAATGTTAAGAACCAGGATACGTGTTGG
EST: gi|22490485|gb|BU050408.1|BU050408
EST:     GGTGATGATGTCGTTCATAAGCTATTTACTGAGCTGGCCTTCCGCTACAG                         AGATCGAGCTGGGGGCTACACAAGAATGTTAAGAACCAGGATACGTGTTGG
genomic: GGTGATGATGTCGTTCATAAGCTATTTACTGAGCTGGCCTTTCGCTACAGgtaatctgtt ... tatattccagAGATCGAGCTGGGGGCTACACAAGAATGTTAAGAACCAGGATACGTGTTGG
EST: gi|21987795|gb|BQ779323.1|BQ779323
EST:     GG-GATGATGTCGTTCATAAGCTATTTACTGAGCTGGCCTTTCGCTACAG                         AGATCGAGCTGGGGGCTACACAAGAATGTTAAGAACCAGGATACGTGTTGG
genomic: GGTGATGATGTCGTTCATAAGCTATTTACTGAGCTGGCCTTTCGCTACAGgtaatctgtt ... tatattccagAGATCGAGCTGGGGGCTACACAAGAATGTTAAGAACCAGGATACGTGTTGG
EST: gi|32929716|gb|CF034528.1|CF034528
EST:     GGTGATGATGTCGTTCATAAGCTATTTACTGAGCTGGCCTTTCGCTACAG                         AGATCGAGCTGGGGGCTACACAAGAATGTTAAGAACCAGGATACGTGTTGG
genomic: GGTGATGATGTCGTTCATAAGCTATTTACTGAGCTGGCCTTTCGCTACAGgtaatctgtt ... tatattccagAGATCGAGCTGGGGGCTACACAAGAATGTTAAGAACCAGGATACGTGTTGG
EST: gi|60397912|gb|DN230728.1|DN230728
EST:     GGTGATGATGTCGTTCATAAGCTATTTACTGAGCTGGCCTTTCGCTACAG                         AGATCGAGCTGGGGGCTACACAAGAATGTTAAGAACCAGGATACGTGTTGG
genomic: GGTGATGATGTCGTTCATAAGCTATTTACTGAGCTGGCCTTTCGCTACAGgtaatctgtt ... tatattccagAGATCGAGCTGGGGGCTACACAAGAATGTTAAGAACCAGGATACGTGTTGG
EST: gi|87151864|gb|DY396653.1|DY396653
EST:     GGTGATGATGTCGTTCATAAGCTATTTACTGAGCTGGCCTTCCGCTACAG                         AGATCGAGCTGGGGGCTACACAAGAATGTTAAGAACCAGGATACGTGTTGG
genomic: GGTGATGATGTCGTTCATAAGCTATTTACTGAGCTGGCCTTTCGCTACAGgtaatctgtt ... tatattccagAGATCGAGCTGGGGGCTACACAAGAATGTTAAGAACCAGGATACGTGTTGG
EST: gi|18965108|gb|BM661397.1|BM661397
EST:     GGTGATGATGTCGTTCATAAGCTATTTACTGAGCTGGCCTTCCGCTACAG                         AGATCGAGCTGGGGGCTACACAAGAATGTTAAGAACCAGGATACGTGTTGG
genomic: GGTGATGATGTCGTTCATAAGCTATTTACTGAGCTGGCCTTTCGCTACAGgtaatctgtt ... tatattccagAGATCGAGCTGGGGGCTACACAAGAATGTTAAGAACCAGGATACGTGTTGG
EST: gi|50337603|gb|CO532729.1|CO532729
EST:     GGTGATGATGTCGTTCATAAGCTATTTACTGAGCTGGCCTTTCGCTACAG                         AGATCGAGCTGGGGGCTACACAAGAATGTTAAGAACCAGGATACGTGTTGG
genomic: GGTGATGATGTCGTTCATAAGCTATTTACTGAGCTGGCCTTTCGCTACAGgtaatctgtt ... tatattccagAGATCGAGCTGGGGGCTACACAAGAATGTTAAGAACCAGGATACGTGTTGG
EST: gi|19058032|gb|BM736699.1|BM736699
EST:     GGTGATGATGTCGTTCATAAGCTATTTACTGAGCTGGCCTTCCGCTACAG                         AGATCGAGCTGGGGGCTA
genomic: GGTGATGATGTCGTTCATAAGCTATTTACTGAGCTGGCCTTTCGCTACAGgtaatctgtt ... tatattccagAGATCGAGCTGGGGGCTA
EST: gi|148963908|gb|EE015020.2|EE015020
EST:     GGTGATGATGTCGTTCATAAGCTATTTACTGAGCTGGCCTTTCGCTACAG                         AGATCGAGCTGGGGGCTACACAAGAATGTTAAGAACCAGGATACGTGTTGG
genomic: GGTGATGATGTCGTTCATAAGCTATTTACTGAGCTGGCCTTTCGCTACAGgtaatctgtt ... tatattccagAGATCGAGCTGGGGGCTACACAAGAATGTTAAGAACCAGGATACGTGTTGG
EST: gi|166482064|gb|EG123746.1|EG123746
EST:     GTGATGATGTCGTTCATAAGCTATTTACTGAGCTGGCCTTCCGCTACAG                         AGATCGAGCTGGGGGCTACACAAGAATGTTAAGAACCAGGATACGTGTTGG
genomic: GTGATGATGTCGTTCATAAGCTATTTACTGAGCTGGCCTTTCGCTACAGgtaatctgtt ... tatattccagAGATCGAGCTGGGGGCTACACAAGAATGTTAAGAACCAGGATACGTGTTGG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 186

GGTACTCAGCATGCAGCAAGACGTGCTGCTGCCTTTGTTCGGGGTGATGATGTCGTTCATAAGCTATTTACTGAGCTGGCCTTTCGCTACAGgtaatctgtt ... tatattccagAGATCGAGCTGGGGGCTACACAAGAATGTTAAGAACCAGGATACGTGTTGGTGATGCTGCTCCAATGGCATACATCGA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 157

GGTACTCAGCATGCAGCAAGACGTGCTGCTGCCTTTGTTCGGGGTGATGATGTCGTTCATAAGCTATTTACTGAGCTGGCCTTTCGCTACAGgtaatctgtt ... tatattccagAGATCGAGCTGGGGGCTACACAAGAATGTTAAGAACCAGGATACGTGTTGGTGATGCTGCTCCAATGGCATACATCGA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 138

GGTACTCAGCATGCAGCAAGACGTGCTGCTGCCTTTGTTCGGGGTGATGATGTCGTTCATAAGCTATTTACTGAGCTGGCCTTTCGCTACAGgtaatctgtt ... tatattccagAGATCGAGCTGGGGGCTACACAAGAATGTTAAGAACCAGGATACGTGTTGGTGATGCTGCTCCAATGGCATACATCGA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 177

GGTACTCAGCATGCAGCAAGACGTGCTGCTGCCTTTGTTCGGGGTGATGATGTCGTTCATAAGCTATTTACTGAGCTGGCCTTTCGCTACAGgtaatctgtt ... tatattccagAGATCGAGCTGGGGGCTACACAAGAATGTTAAGAACCAGGATACGTGTTGGTGATGCTGCTCCAATGGCATACATCGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccatgtatttggaagcagagtggattggaactaattgtatatttttatattccagAGATCGAGCTGGGGGCTACACAAGAATGTTAAGAACCAGGATACGTGTTGGTGATGCTGCTCCAATGGCATACATCGA
                            aactaat  putative branch site (score: 177)
                                       tattttt  putative PPT
                       attggaactaattgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taatggtttgtatgataacacaaatgtgaaaagtagaatagaatgccatgtatttggaagcagagtggattggaactaattgtatatttttatattccagAGATCGAGCTGGGGGCTACACAAGAATGTTAAGAACCAGGATACGTGTTGGTGATGCTGCTCCAATGGCATACATCGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - -ttgtatg
- - - - - - - - -acacaaa
- - - - - - - - - - - - - -gaaaagta
- - - - - - - - - - - - - - - - - - - -agaatgc
- - - - - - - - - - - - - - - - - - - - - - - catgtat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - gaagcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaactaa