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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagcctatggatatattcttgtactttttctccctatcatatctgatcttgtagtagtagttaacttcattcttctgtatgcagCATTATGTTTGGACCAGATATCTGTGGGTACAGCACCAAGAAGGTTCACACTATCCTGACAAAGGATGGCAAGAACCACTTGATCAAGAAGGATGTGCCT

Basic information

species Zea mays
transcript GRMZM2G074687_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G074687_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os07g14270.3 (Oryza sativa), 3'ss of exon 3
gtagcc-tatggatatattcttgtactttttctccctatcatatctgatcttgtagtagt-agttaacttcattcttctgtatgcagCATTATGTTTGGACCAGATATCTGTGGGTACAGCACCAAGAAGGTTCACACTATCCTGACAAAGGATGGCAAGAACCACTTGATCAAGAAGGATGTGCCT
|||    | |   | |||| | |  ||  ||||| || |  | ||     | ||| |||| |  ||||||  | ||| || |||||||||||||||||||||||| |||||||||||||||||||||||||| || |||||| | || ||| ||| ||||||||| ||||||||||||||||| || 
gtaatgattttcttctattgtagctctgattctcacttt--tctcaagattagtactagttatctaacttggtacttttgaatgcagCATTATGTTTGGACCAGACATCTGTGGGTACAGCACCAAGAAGGTCCATACTATCTTTACTAAGAATGACAAGAACCATTTGATCAAGAAGGATGTCCCC

upper sequence: GRMZM2G074687_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA20G23080.2 (Glycine max), 3'ss of exon 3
gtagcctatggatatattcttg------tactttttctc--------cctatcatatctgatcttgtagtagtagttaac-ttcattcttctgtatgcagCATTATGTTTGGACCAGATATCTGTGGGTACAGCACCAAGAAGGTTCACACTATCCTGACAAAGGATGGCAAGAACCACTTGATCAAGAAGGATGTGCCT
||    |||  ||    | |||      | || ||||          ||| |||||||  |         |    ||||| ||  || |||||| ||||| ||||||||||| |||||||||||||| ||||| || ||||| || ||| |||| || ||  |  ||| ||  ||||||||||| ||||||||||| |||
gtgatttatatatccccttttgatttgttgctctttcctgatgggtgcctctcatatcgcaaaacacctgaccttttaacatttgttgttctgt-tgcagTATTATGTTTGGCCCAGATATCTGTGGTTACAGTACAAAGAAAGTACACGCTATTCTTACCTACAATGACACAAACCACTTGATAAAGAAGGATGTTCCT

upper sequence: GRMZM2G074687_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA10G28890.1 (Glycine max), 3'ss of exon 3
gtagcctatggatatattcttg---tactttttctccctatcatat----ctgatcttgtag--tagtag-----ttaac-ttcattcttctgtatgcagCATTATGTTTGGACCAGATATCTGTGGGTACAGCACCAAGAAGGTTCACACTATCCTGACAAAGGATGGCAAGAACCACTTGATCAAGAAGGATGTGCCT
||    |||  ||    | |||   | ||  |  | |||      |     |||| |||||    ||  |     || || ||  || |||||| ||||| ||||||||||| ||||||||||| || ||||| |||||||| |||||| |||| || ||  |  ||  ||  ||||||||||| ||||||||||| |||
gtgatttatatatccccttttgatttgctgctctttcctgatgggtgcctttgatgttgtaaaacagctgatcttttgacatttgttgttctgt-tgcagTATTATGTTTGGCCCAGATATCTGCGGTTACAGTACCAAGAAAGTTCACGCTATTCTTACCTACAATAACACAAACCACTTGATAAAGAAGGATGTTCCT

upper sequence: GRMZM2G074687_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT1G56340.1 (Arabidopsis thaliana), 3'ss of exon 3
gtagcctatggatatattcttgtactttttctccctatcatatctgatcttgtagtagtag--ttaacttcattcttctgtatgcagCATTATGTTTGGACCAGATATCTGTGGGTACAGCACCAAGAAGGTTCACACTATCCTGACAAAGGATGGCAAGAACCACTTGATCAAGAAGGATGTGCCT
            | | || ||    |  ||     |   |  ||  |  ||  |  |  ||  ||| |||  || || | | ||||||||||||||||| |||||||| ||||| |||||||| ||||| || ||  ||||||| ||  |  |||| |  ||||| |||||||||||||| || || 
-----------gtgtgtttttcggttactttcatatcaaacttcaaacattcaaacaccaggcttatctttctttttttatctgcagCATTATGTTTGGGCCAGATATTTGTGGCTACAGCACTAAGAAAGTACATGCTATCCTTACTTACAATGGAACCAACCATTTGATCAAGAAGGAGGTCCCA

upper sequence: GRMZM2G074687_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv14s0060g01290.t01 (Vitis vinifera), 3'ss of exon 3
---------------gtagcctatggatatattcttgtactttttctccctatcatatctgatcttgtagtagtagttaacttcattct---tctgtatgcagCATTATGTTTGGACCAGATATCTGTGGGTACAGCACCAAGAAGGTTCACACTATCCTGACAAAGGATGGCAAGAACCACTTGATCAAGAAGGATGTGCCT
               |    || |   | | | | | |   | |    || | | | |     ||| ||  ||| ||| | ||  |        ||  |||||||| ||||||||||| ||||||||||| || | |||||| ||||| ||  |||| || |||   ||||| || || ||||| || ||||||||||| |||
gtcagtgttatttttgcttactgtttgtttgtccctttgtctatgactccaaacttcttatcccttttaa-agttgttgatttgttataaaacatgattgcagCATCATGTTTGGACCTGATATCTGTGGCTATACCACCAAAAAGGTCCATGCTATTCTTACACGAGATGGAAAAAATCACTTAATTAAGAAGGATGTTCCT

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|148948737|gb|EC898659.2|EC898659
EST:     CTGGGTGGTGATGTAGACCAGAAAAAATTCGGTGGGGACACAACTTACAG                         CATTATGTTTGGACCAGATATCTGTGGGTACAGCACCAAGAAGGTTCACAC
genomic: CTGGGTGGTGATGTAGACCAGAAAAAATTCGGTGGGGACACAACTTACAGgtagcctatg ... ctgtatgcagCATTATGTTTGGACCAGATATCTGTGGGTACAGCACCAAGAAGGTTCACAC
EST: gi|149008411|gb|EE040568.2|EE040568
EST:     CTGGGTGGTGATGTAGACCAGAAAAAATTCGGTGGGGACACAACTTACAG                         CATTATGTTTGGACCAGATATCTGTGGGTACAGCACCAAGAAGGTTCACAC
genomic: CTGGGTGGTGATGTAGACCAGAAAAAATTCGGTGGGGACACAACTTACAGgtagcctatg ... ctgtatgcagCATTATGTTTGGACCAGATATCTGTGGGTACAGCACCAAGAAGGTTCACAC
EST: gi|58029459|gb|CX724886.1|CX724886
EST:     CTGGGTGGTGATGTAGACCAGAAAAAATTCGGTGGGGACACAACTTACAG                         CATTATGTTTGGACCAGATATCTGTGGGTACAGCACCAAGAAGGTTCACAC
genomic: CTGGGTGGTGATGTAGACCAGAAAAAATTCGGTGGGGACACAACTTACAGgtagcctatg ... ctgtatgcagCATTATGTTTGGACCAGATATCTGTGGGTACAGCACCAAGAAGGTTCACAC
EST: gi|149014111|gb|EE043648.2|EE043648
EST:     CTGGGTGGTGATGTAGACCAGAAAAAATTCGGTGGGGACACAACTTACAG                         CATTATGTTTGGACCAGATATCTGTGGGTACAGCACCAAGAAGGTTCACAC
genomic: CTGGGTGGTGATGTAGACCAGAAAAAATTCGGTGGGGACACAACTTACAGgtagcctatg ... ctgtatgcagCATTATGTTTGGACCAGATATCTGTGGGTACAGCACCAAGAAGGTTCACAC
EST: gi|31558809|gb|CD528021.1|CD528021
EST:     CTGGGTGGTGATGTAGACCAGAAAAAATTCGGTGGGGACACAACTTACAG                         CATTATGTTTGGACCAGATATCTGTGGGTACAGCACCAAGAAGGGTCACAC
genomic: CTGGGTGGTGATGTAGACCAGAAAAAATTCGGTGGGGACACAACTTACAGgtagcctatg ... ctgtatgcagCATTATGTTTGGACCAGATATCTGTGGGTACAGCACCAAGAAGGTTCACAC
EST: gi|148935865|gb|EC879913.2|EC879913
EST:     CTGGGTGGTGATGTAGACCAGAAAAAATTCGGTGGGGACACAACTTACAG                         CATTATGTTTGGACCAGATATCTGTGGGTACAGCACCAAGAAGGTTCACAC
genomic: CTGGGTGGTGATGTAGACCAGAAAAAATTCGGTGGGGACACAACTTACAGgtagcctatg ... ctgtatgcagCATTATGTTTGGACCAGATATCTGTGGGTACAGCACCAAGAAGGTTCACAC
EST: gi|149097674|gb|EE183578.2|EE183578
EST:     CTGGGTGGTGATGTAGACCAGAAAAAATTCGGTGGGGACACAACTTACAG                         CATTATGTTTGGACCAGATATCTGTGGGTACAGCACCAAGAAGGTTCACAC
genomic: CTGGGTGGTGATGTAGACCAGAAAAAATTCGGTGGGGACACAACTTACAGgtagcctatg ... ctgtatgcagCATTATGTTTGGACCAGATATCTGTGGGTACAGCACCAAGAAGGTTCACAC
EST: gi|148959988|gb|EE153227.2|EE153227
EST:     CTGGGTGGTGATGTAGACCAGAAAAAATTCGGTGGGGACACAACTTACAG                         CATTATGTTTGGACCAGATATCTGTGGGTACAGCACCAAGAAGGTTCACAC
genomic: CTGGGTGGTGATGTAGACCAGAAAAAATTCGGTGGGGACACAACTTACAGgtagcctatg ... ctgtatgcagCATTATGTTTGGACCAGATATCTGTGGGTACAGCACCAAGAAGGTTCACAC
EST: gi|149112807|gb|EE295617.2|EE295617
EST:     CTGGGTGGTGATGTAGACCAGAAAAAATTCGGTGGGGACACAACTTACAG                         CATTATGTTTGGACCAGATATCTGTGGGTACAGCACCAAGAAGGTTCACAC
genomic: CTGGGTGGTGATGTAGACCAGAAAAAATTCGGTGGGGACACAACTTACAGgtagcctatg ... ctgtatgcagCATTATGTTTGGACCAGATATCTGTGGGTACAGCACCAAGAAGGTTCACAC
EST: gi|149011835|gb|EE042440.2|EE042440
EST:     CTGGGTGGTGATGTAGACCAGAAAAAATTCGGTGGGGACACAACTTACAG                         CATTATGTTTGGACCAGATATCTGTGGGTACAGCACCAAGAAGGTTCACAC
genomic: CTGGGTGGTGATGTAGACCAGAAAAAATTCGGTGGGGACACAACTTACAGgtagcctatg ... ctgtatgcagCATTATGTTTGGACCAGATATCTGTGGGTACAGCACCAAGAAGGTTCACAC
EST: gi|149084306|gb|EE173743.2|EE173743
EST:     CTGGGTGGTGATGTAGACCAGAAAAAATTCGGTGGGGACACAACTTACAG                         CATTATGTTTGGACCAGATATCTGTGGGTACAGCACCAAGAAGGTTCACAC
genomic: CTGGGTGGTGATGTAGACCAGAAAAAATTCGGTGGGGACACAACTTACAGgtagcctatg ... ctgtatgcagCATTATGTTTGGACCAGATATCTGTGGGTACAGCACCAAGAAGGTTCACAC
EST: gi|148935504|gb|EC879545.2|EC879545
EST:     CTGGGTGGTGATGTAGACCAGAAAAAATTCGGTGGGGACACAACTTACAG                         CATTATGTTTGGACCAGATATCTGTGGGTACAGCACCAAGAAGGTTCACAC
genomic: CTGGGTGGTGATGTAGACCAGAAAAAATTCGGTGGGGACACAACTTACAGgtagcctatg ... ctgtatgcagCATTATGTTTGGACCAGATATCTGTGGGTACAGCACCAAGAAGGTTCACAC
EST: gi|60672264|gb|DN475030.1|DN475030
EST:     GGGACACAACTTACAG                         CATTATGTTTGGACCAGATATCTGTGGGTACAGCACCAAGAAGGTTCACAC
genomic: GGGACACAACTTACAGgtagcctatg ... ctgtatgcagCATTATGTTTGGACCAGATATCTGTGGGTACAGCACCAAGAAGGTTCACAC

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: 42 (upstream exon), 48 (downstream exon)
Score: 78

CTGTGAAGCACGAGCAGAAGCTTGACTGTGGTGGTGGTTACGTCAAGTTGCTGGGTGGTGATGTAGACCAGAAAAAATTCGGTGGGGACACAACTTACAGgtagcctatg ... ctgtatgcagCATTATGTTTGGACCAGATATCTGTGGGTACAGCACCAAGAAGGTTCACACTATCCTGACAAAGGATGGCAAGAACCACTTGATCAAGAAGGATGTGCCT


Block sizes: 42 (upstream exon), 48 (downstream exon)
Score: 223

CTGTGAAGCACGAGCAGAAGCTTGACTGTGGTGGTGGTTACGTCAAGTTGCTGGGTGGTGATGTAGACCAGAAAAAATTCGGTGGGGACACAACTTACAGgtagcctatg ... ctgtatgcagCATTATGTTTGGACCAGATATCTGTGGGTACAGCACCAAGAAGGTTCACACTATCCTGACAAAGGATGGCAAGAACCACTTGATCAAGAAGGATGTGCCT


Block sizes: 42 (upstream exon), 48 (downstream exon)
Score: 166

CTGTGAAGCACGAGCAGAAGCTTGACTGTGGTGGTGGTTACGTCAAGTTGCTGGGTGGTGATGTAGACCAGAAAAAATTCGGTGGGGACACAACTTACAGgtagcctatg ... ctgtatgcagCATTATGTTTGGACCAGATATCTGTGGGTACAGCACCAAGAAGGTTCACACTATCCTGACAAAGGATGGCAAGAACCACTTGATCAAGAAGGATGTGCCT


Block sizes: 42 (upstream exon), 48 (downstream exon)
Score: 1336

CTGTGAAGCACGAGCAGAAGCTTGACTGTGGTGGTGGTTACGTCAAGTTGCTGGGTGGTGATGTAGACCAGAAAAAATTCGGTGGGGACACAACTTACAGgtagcctatg ... ctgtatgcagCATTATGTTTGGACCAGATATCTGTGGGTACAGCACCAAGAAGGTTCACACTATCCTGACAAAGGATGGCAAGAACCACTTGATCAAGAAGGATGTGCCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctccctatcatatctgatcttgtagtagtagttaacttcattcttctgtatgcagCATTATGTTTGGACCAGATATCTGTGGGTACAGCACCAAGAAGGTTCACACTATCCTGACAAAGGATGGCAAGAACCACTTGATCAAGAAGGATGTGCCT
                             agttaac  putative branch site (score: 1336)
                                   cttcattcttctgt  CT-rich tract
     tatcatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagcctatggatatattcttgtactttttctccctatcatatctgatcttgtagtagtagttaacttcattcttctgtatgcagCATTATGTTTGGACCAGATATCTGTGGGTACAGCACCAAGAAGGTTCACACTATCCTGACAAAGGATGGCAAGAACCACTTGATCAAGAAGGATGTGCCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG