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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATTAGGTCCTACCATGGGCATCTGAGTGGTGTTTACTGCCTAGCTCTCCATCCAACAATTGATATCTTACTGACTGGTGGCCGGGATTCAGTTTGCAGGgtatgatctctcttgcagttgcaccttctgaaaaatctcatcgtattcaatgatcacttggttttacttgggttatatgtacag

Basic information

species Zea mays
transcript GRMZM2G017089_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G017089_T02 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os03g21990.1 (Oryza sativa), 5'ss of exon 11
TATTAGGTCCTACCATGGGCATCTGAGTGGTGTTTACTGCCTAGCTCTCCATCCAACAATTGATATCTTACTGACTGGTGGCCGGGATTCAGTTTGCAGGgtat--gatc-tctcttgcagttgcaccttctgaaaaatct--------catcgtattcaatgatcacttggttttacttgggttatatgtacag
||||||||| || ||||| ||| ||||||| || |||||||| ||||| ||||||||||| |||||||| ||||||||||| || ||||||||||| |||||||   |||  |||||  | ||  | ||| || | ||||         ||| ||| | |   |    | ||||||   ||   |  ||  ||||
TATTAGGTCTTATCATGGCCATTTGAGTGGGGTGTACTGCCTTGCTCTACATCCAACAATCGATATCTTGCTGACTGGTGGTCGCGATTCAGTTTGTAGGgtatataatcacctcttttatttatatcttatgcataatcattagcatacattgtactaaggtaggtttgggtttttgctgaccttcatacacag

upper sequence: GRMZM2G017089_T02 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA09G04910.1 (Glycine max), 5'ss of exon 10
TATTAGGTCCTACCATGGGCATCTGAGTGGTGTTTACTGCCTAGCTCTCCATCCAACAATTGATATCTTACTGACTGGTGGCCGGGATTCAGTTTGCAGGgtatgatctctcttgcagttgcacc-ttctgaaaaatctcatcgtattcaatgatcacttggttttacttgggttatatgtacag----------------------------------------------------------
||||||||| || ||||| ||||||||||||||||| ||| | ||||| ||||| ||||||||  | ||||| || || || || ||||| || ||| |||||||   | |  ||   | |   | || | | | |  | |  | ||   ||  |  || |    || ||  |  |||| | ||                                                           
TATTAGGTCTTATCATGGTCATCTGAGTGGTGTTTATTGCTTGGCTCTTCATCCCACAATTGACGTTTTACTAACCGGAGGACGTGATTCTGTCTGCCGGgtatggattttgctgatatagtttcattattatataattaaatgaatgtgatcctttctggcaaataattccga-atattttcaaatttcttattaaggaatagaaatgtaaaattcatactttggtgatgctcaattttcag

upper sequence: GRMZM2G017089_T02 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA15G15960.1 (Glycine max), 5'ss of exon 10
TATTAGGTCCTACCATGGGCATCTGAGTGGTGTTTACTGCCTAGCTCTCCATCCAACAATTGATATCTTACTGACTGGTGGCCGGGATTCAGTTTGCAGGgtatg-atctctcttgcag----------ttgcaccttctgaaaaatctcatcgtattcaatgatcactt--ggttttacttgggttatatgtacag---------------------------------------------
|||||| || || ||||| ||||||||||||||||| ||| | ||||| ||||| ||||||||  | ||||| || || || || ||||| || ||| ||||||| || |  ||   ||          ||| |   |  ||  ||| | ||| | |    | |  | ||  |  | |  |    ||   | |  ||                                             
TATTAGATCTTATCATGGTCATCTGAGTGGTGTTTATTGCTTGGCTCTTCATCCCACAATTGACGTTTTACTAACCGGAGGACGTGATTCTGTCTGCCGGgtatggattttgctgatagagtttcattattgtatagttagatgaatgtgatcctttctggtaaataatttcgaatattttcaaatttgttattaaggaatagaaatgtaaaatttatgctttggtgatgctaaattttcag

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|71432304|gb|DR813354.1|DR813354
EST:     ATCCAACAATTGATATCTTACTGACTGGTGGCCGGGATTCAGTTTGCAGG                         GTGTGGGACATCAGAACAAAAGCACATGTTTCTGCTTTAACAGGGCATGAC
genomic: ATCCAACAATTGATATCTTACTGACTGGTGGCCGGGATTCAGTTTGCAGGgtatgatctc ... atatgtacagGTGTGGGACATCAGAACAAAAGCACATGTTTCTGCTTTAACAGGGCATGAC
EST: gi|6021220|gb|AW066148.1|AW066148
EST:     ATCCAACAATTGATATCTTACTGACTGGTGGCCGGGATTCAGTTTGCAGG                         GTGTGGGACATCAGAACAAAAGCACATGTTTCTGCTTTAACAGGGCATGAC
genomic: ATCCAACAATTGATATCTTACTGACTGGTGGCCGGGATTCAGTTTGCAGGgtatgatctc ... atatgtacagGTGTGGGACATCAGAACAAAAGCACATGTTTCTGCTTTAACAGGGCATGAC
EST: gi|32933221|gb|CF038033.1|CF038033
EST:     ATCCAACAATTGATATCTTACTGACTGGTGGCCGGGATTCAGTTTGCAGG                         GTGTGGGACATCAGAACAAAAGCACATGTTTCTGCTTTAACAGGGCATGAC
genomic: ATCCAACAATTGATATCTTACTGACTGGTGGCCGGGATTCAGTTTGCAGGgtatgatctc ... atatgtacagGTGTGGGACATCAGAACAAAAGCACATGTTTCTGCTTTAACAGGGCATGAC
EST: gi|211016045|gb|FL237689.1|FL237689
EST:     ATCCAACAATTGATATCTTACTGACTGGTGGCCGGGATTCAGTTTGCAGG                         GTGTGGGACATCAGAACAAAAGCACATGTTTCTGCTTTAACAGGGCATGAC
genomic: ATCCAACAATTGATATCTTACTGACTGGTGGCCGGGATTCAGTTTGCAGGgtatgatctc ... atatgtacagGTGTGGGACATCAGAACAAAAGCACATGTTTCTGCTTTAACAGGGCATGAC
EST: gi|148943610|gb|EC888673.2|EC888673
EST:     ATTCAGTTTGCAGG                         GTG-GGGACATCAGAACAAAAGCACATGTTTCTGCTTTAACAGGGCATGAC
genomic: ATTCAGTTTGCAGGgtatgatctc ... atatgtacagGTGTGGGACATCAGAACAAAAGCACATGTTTCTGCTTTAACAGGGCATGAC

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: 48 (upstream exon), 49 (downstream exon)
Score: 205

TATTAGGTCCTACCATGGGCATCTGAGTGGTGTTTACTGCCTAGCTCTCCATCCAACAATTGATATCTTACTGACTGGTGGCCGGGATTCAGTTTGCAGGgtatgatctc ... atatgtacagGTGTGGGACATCAGAACAAAAGCACATGTTTCTGCTTTAACAGGGCATGACAACACTGTCTGTTCAGTGTTTGCTCGTCCTACG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 104

TATTAGGTCCTACCATGGGCATCTGAGTGGTGTTTACTGCCTAGCTCTCCATCCAACAATTGATATCTTACTGACTGGTGGCCGGGATTCAGTTTGCAGGgtatgatctc ... atatgtacagGTGTGGGACATCAGAACAAAAGCACATGTTTCTGCTTTAACAGGGCATGACAACACTGTCTGTTCAGTGTTTGCTCGTCCTACG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 98

TATTAGGTCCTACCATGGGCATCTGAGTGGTGTTTACTGCCTAGCTCTCCATCCAACAATTGATATCTTACTGACTGGTGGCCGGGATTCAGTTTGCAGGgtatgatctc ... atatgtacagGTGTGGGACATCAGAACAAAAGCACATGTTTCTGCTTTAACAGGGCATGACAACACTGTCTGTTCAGTGTTTGCTCGTCCTACG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 82

TATTAGGTCCTACCATGGGCATCTGAGTGGTGTTTACTGCCTAGCTCTCCATCCAACAATTGATATCTTACTGACTGGTGGCCGGGATTCAGTTTGCAGGgtatgatctc ... atatgtacagGTGTGGGACATCAGAACAAAAGCACATGTTTCTGCTTTAACAGGGCATGACAACACTGTCTGTTCAGTGTTTGCTCGTCCTACG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TATTAGGTCCTACCATGGGCATCTGAGTGGTGTTTACTGCCTAGCTCTCCATCCAACAATTGATATCTTACTGACTGGTGGCCGGGATTCAGTTTGCAGGgtatgatctctcttgcagttgcaccttctgaaaaatctcatcgtattcaatgatcacttggttttacttgggttatatgtacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG