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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaaaatgctaatccaatgcaaaaacagggggctactcttatgtggttttataaggtcttctttgcttttatcaataacagacttattttcctggatgcagCACACACACTGAAGTGCAGGAGAGAGTGCTGAAGGGAAGGATGGACTGATGAGTGCTGCCATGTAGTTATTCTAGGAGAGATTGTTTCTTCATTCGCCCT

Basic information

species Zea mays
transcript GRMZM2G117544_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G117544_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os02g08520.1 (Oryza sativa), 3'ss of exon 6
------------gaaaatgctaatccaatgcaaaaacagggggctactcttatgtggttttataaggtcttctttgcttttatcaa---taacagacttattttcctgg-----------atgcagCACACACACTGAAGTGCAGGAGAGAGTGCTGAAGGGAAGGATGGACTGATGAGTGCTGCCATGTAGTTA--TTCTAGGAGAGATTGTTTCTTCATTCGCCCT
             |  ||  |  | || |   |  | |   ||    |   |||     |  ||| |   || |||   |||   |   |   | | || |||||||||           |||||| || | ||| || || |||||||||||| | |||||||||||||||||| | |  |  || |  |  ||  |       | ||| |||  ||| ||||  | 
gtaagttccatatatgatcatttttcactcacactaaacatgggagtttagatgaaaactc-taatgctgtcgttgtccttactgaatctgtgaaatttgttttcctggcttgttggttaatgcagGACTCCCACAGAGGTTCAGGAGAGAGTGATCAAGGGAAGGATGGACTGA-GTGCTCGCCCGTAGACCTAGATCGCGTAGGGGATGGTTCGTTCGTTCGATC-
















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|32844693|gb|CD984374.1|CD984374
EST:     TCTGGTGATCGCGACTGCCTCAGCGGCTGGGGAGGTTATGTTCTTGTTGT                         CACACCCACTGAAGTGCAGGAGAGAGTGCTGAAGGGAAGGATGGACTGATG
genomic: TCTGTTGATCGCGACTGCCTCAGCGGCTGGGGAGGTTATGTTCTTGTTGTgtaagttccc ... ctggatgcagCACACACACTGAAGTGCAGGAGAGAGTGCTGAAGGGAAGGATGGACTGATG
EST: gi|88758274|gb|DY542415.1|DY542415
EST:     TCTGTTGATCGCGACTGCCTCAGCGGCTGGGGAGGTTATGTTCTTGTTGT                         CACACACACTGAAGTGCAGGAGAGAGTGCTGAAGGGAAGGATGGACTGATG
genomic: TCTGTTGATCGCGACTGCCTCAGCGGCTGGGGAGGTTATGTTCTTGTTGTgtaagttccc ... ctggatgcagCACACACACTGAAGTGCAGGAGAGAGTGCTGAAGGGAAGGATGGACTGATG
EST: gi|94476825|gb|EB705783.1|EB705783
EST:     TCTGTTGATCGCGACTGCCTCAGCGGCTGGGGAGGTTATGTTCTTGTTGT                         CACACACACTGAAGTGCAGGAGAGAGTGCTGAAGGGAAGGATGGACTGATG
genomic: TCTGTTGATCGCGACTGCCTCAGCGGCTGGGGAGGTTATGTTCTTGTTGTgtaagttccc ... ctggatgcagCACACACACTGAAGTGCAGGAGAGAGTGCTGAAGGGAAGGATGGACTGATG
EST: gi|32848246|gb|CD987927.1|CD987927
EST:     TCTGTT-ATCGCGACTGCCTCAGCGGCTGGGGAGGTCATGTTCTTGTTGT                         CACACCCACTGAAGTGCAGGAGAGAGTGCTGAAGGGAAGGATGGACTGATG
genomic: TCTGTTGATCGCGACTGCCTCAGCGGCTGGGGAGGTTATGTTCTTGTTGTgtaagttccc ... ctggatgcagCACACACACTGAAGTGCAGGAGAGAGTGCTGAAGGGAAGGATGGACTGATG
EST: gi|32844036|gb|CD983717.1|CD983717
EST:     TCTGTTGATCGCGACTGCCTCAGCGGCTGGGGAGGTTATGTTCTTGTTGT                         CACACCCACTGAAGTGCAGGAGAGAGTGCTGAAGGGAAGGATGGACTGATG
genomic: TCTGTTGATCGCGACTGCCTCAGCGGCTGGGGAGGTTATGTTCTTGTTGTgtaagttccc ... ctggatgcagCACACACACTGAAGTGCAGGAGAGAGTGCTGAAGGGAAGGATGGACTGATG
EST: gi|166616877|gb|EG290576.1|EG290576
EST:     CAGCGGCTGGGGAGGTTATGTTCTTGTTGT                         CACACCCACTGAAGTGCAGGAGAGAGTGCTGAAGGGAAGGATGGACTGATG
genomic: CAGCGGCTGGGGAGGTTATGTTCTTGTTGTgtaagttccc ... ctggatgcagCACACACACTGAAGTGCAGGAGAGAGTGCTGAAGGGAAGGATGGACTGATG
EST: gi|211034562|gb|FL157508.1|FL157508
EST:     TCTGTTGATCGCGACTGCCTCAGTGGCTGGGGAGGTTATGTTCTTGTTGT                         CACACCCACTGAAGTGCAGGAGAGAGTGCTGAAGGGAAGGATGGACTGATG
genomic: TCTGTTGATCGCGACTGCCTCAGCGGCTGGGGAGGTTATGTTCTTGTTGTgtaagttccc ... ctggatgcagCACACACACTGAAGTGCAGGAGAGAGTGCTGAAGGGAAGGATGGACTGATG
EST: gi|32845419|gb|CD985100.1|CD985100
EST:     TCTGTTGATCGCGACTGCCTCAGCGGCTGGGGAGGTTATGTTCTTGTTGT                         CACACCCACTGAAGTGCAGGAGAGAGTGCTGAAGGGAAGGATGGACTGATG
genomic: TCTGTTGATCGCGACTGCCTCAGCGGCTGGGGAGGTTATGTTCTTGTTGTgtaagttccc ... ctggatgcagCACACACACTGAAGTGCAGGAGAGAGTGCTGAAGGGAAGGATGGACTGATG
EST: gi|30088206|gb|CB886411.1|CB886411
EST:     TCTGTTGATCGCGACTGCCTCAGCGGCTGGGGAGGTTATGTTCTTGTTGT                         CACACACACTGAAGTGCAGGAGAGAGTGCTGAAGGGAAGGATGGACTGATG
genomic: TCTGTTGATCGCGACTGCCTCAGCGGCTGGGGAGGTTATGTTCTTGTTGTgtaagttccc ... ctggatgcagCACACACACTGAAGTGCAGGAGAGAGTGCTGAAGGGAAGGATGGACTGATG
EST: gi|88758273|gb|DY542414.1|DY542414
EST:     TCTGTTGATCGCGACTGCCTCAGCGGCTGGGGAGGTTATGTTCTTGTTGT                         CACACACACTGAAGTGCAGGAGAGAGTGCTGAAGGGAAGGATGGACTGATG
genomic: TCTGTTGATCGCGACTGCCTCAGCGGCTGGGGAGGTTATGTTCTTGTTGTgtaagttccc ... ctggatgcagCACACACACTGAAGTGCAGGAGAGAGTGCTGAAGGGAAGGATGGACTGATG

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: 154

GAACCCGAAGAACTTTTCGAGACAATCTCGCAAGCATTGCAGGCATCTGTTGATCGCGACTGCCTCAGCGGCTGGGGAGGTTATGTTCTTGTTGTgtaagttccc ... ctggatgcagCACACACACTGAAGTGCAGGAGAGAGTGCTGAAGGGAAGGATGGACTGATGAGTGCTGCCATGTAGTTATTCTAGGAGAGATTGTTTCTTCATTCGCCCT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 92

GAACCCGAAGAACTTTTCGAGACAATCTCGCAAGCATTGCAGGCATCTGTTGATCGCGACTGCCTCAGCGGCTGGGGAGGTTATGTTCTTGTTGTgtaagttccc ... ctggatgcagCACACACACTGAAGTGCAGGAGAGAGTGCTGAAGGGAAGGATGGACTGATGAGTGCTGCCATGTAGTTATTCTAGGAGAGATTGTTTCTTCATTCGCCCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 79

GAACCCGAAGAACTTTTCGAGACAATCTCGCAAGCATTGCAGGCATCTGTTGATCGCGACTGCCTCAGCGGCTGGGGAGGTTATGTTCTTGTTGTgtaagttccc ... ctggatgcagCACACACACTGAAGTGCAGGAGAGAGTGCTGAAGGGAAGGATGGACTGATGAGTGCTGCCATGTAGTTATTCTAGGAGAGATTGTTTCTTCATTCGCCCT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 93

GAACCCGAAGAACTTTTCGAGACAATCTCGCAAGCATTGCAGGCATCTGTTGATCGCGACTGCCTCAGCGGCTGGGGAGGTTATGTTCTTGTTGTgtaagttccc ... ctggatgcagCACACACACTGAAGTGCAGGAGAGAGTGCTGAAGGGAAGGATGGACTGATGAGTGCTGCCATGTAGTTATTCTAGGAGAGATTGTTTCTTCATTCGCCCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttataaggtcttctttgcttttatcaataacagacttattttcctggatgcagCACACACACTGAAGTGCAGGAGAGAGTGCTGAAGGGAAGGATGGACTGATGAGTGCTGCCATGTAGTTATTCTAGGAGAGATTGTTTCTTCATTCGCCCT
                          caataac  putative branch site (score: 93)
                                    cttattttcct  putative PPT
                    ttttatcaataaca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaaaatgctaatccaatgcaaaaacagggggctactcttatgtggttttataaggtcttctttgcttttatcaataacagacttattttcctggatgcagCACACACACTGAAGTGCAGGAGAGAGTGCTGAAGGGAAGGATGGACTGATGAGTGCTGCCATGTAGTTATTCTAGGAGAGATTGTTTCTTCATTCGCCCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - atgctaa
- - - - - - -caatgca
- - - - - - - - - - aaaacagg
- - - - - - - - - - - - - - - gctactc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aataaca