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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgctctgcagtctgcacacactctatttacttctctaagtacgatctcagttgttgaaaaactattgcttacagGACTTCCGACTACGCGACATCAATGAGTATGCTGAGTGGTATGGACATTCCCACAGGGCACCGGAACTTCAG

Basic information

species Zea mays
transcript GRMZM2G038848_T02
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G038848_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os03g42110.1 (Oryza sativa), 3'ss of exon 6
gtatgctctgcagtct--------------gcacacactctatttacttctctaagtacgatctcagttgttgaaaaactat--tgcttacagGACTTCCGACTACGCGACATCAATGAGTATGCTGAGTGGTATGGACATTCCCACAGGGCACCGGAACTTCAG
|||||||||  | |||              | |   |   | | |  ||||  |    | |||    || | |   |  ||   || ||  |||| || ||| | || || ||||||||||| |||||||||||||| ||||| || |||||||| |||||||||
gtatgctctataatctcatgaattttctacgtaggtatcatttctgattcttgacagtcaatcattcttatgggtgacttaccatgtttgtagGATTTTCGATTGCGTGATATCAATGAGTACGCTGAGTGGTATGGCCATTCTCATAGGGCACCAGAACTTCAG

upper sequence: GRMZM2G038848_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os10g35170.1 (Oryza sativa), 3'ss of exon 6
gtatgctctgcag-------------tctgcacacactctatttact----tctctaa-gtacgatctcagt-tgttgaaaaactattgcttacagGACTTCCGACTACGCGACATCAATGAGTATGCTGAGTGGTATGGACATTCCCACAGGGCACCGGAACTTCAG
|||||||   ||              | |||| | |   | | |       | |||||  | |  ||| | |  ||  ||       |  |||||||| |||||  | || || ||||||||||| |||||||||||||| ||| | || |||||||| |||||||||
gtatgcttcacaaggctaacagtttatttgcatagatattgtctttcatgctatctaatatccattcttactacgtctaattgaccatctttacagGATTTCCGTTTGCGTGATATCAATGAGTACGCTGAGTGGTATGGTCATGCACATAGGGCACCAGAACTTCAG
















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|78093374|gb|DV521748.1|DV521748
EST:     AAATTATCAAAAGCTTACCCCGACACTTAAAGATTGTTGATCTCTCAGCG                         GACTTCCGACTACGCGACATCAATGAGTATGCTGAGTGGTATGGACATTCC
genomic: AAATTATCAAAAGCTTACCCCGACACTTAAAGATTGTTGATCTCTCAGCGgtatgctctg ... ttgcttacagGACTTCCGACTACGCGACATCAATGAGTATGCTGAGTGGTATGGACATTCC
EST: gi|31354246|gb|CD438603.1|CD438603
EST:     AAATTATCAAAAGCTTACCCCGACACTTAAAGATTGTTGATCTCTCAGCG                         GACTTCCGACTACGCGACATCAATGAGTATGCTGAGTGGTATGGACATTCC
genomic: AAATTATCAAAAGCTTACCCCGACACTTAAAGATTGTTGATCTCTCAGCGgtatgctctg ... ttgcttacagGACTTCCGACTACGCGACATCAATGAGTATGCTGAGTGGTATGGACATTCC
EST: gi|148943028|gb|EC888078.2|EC888078
EST:     AATTTATCAAAAGCTTACCCCGACACTTAAAGATTGTTGATCTCTCAGCG                         GACTTCCGACTACGCGACATCAATGAGTATGCTGAGTGGTATGGACATTCC
genomic: AATT-ATCAAAAGCTTACCCCGACACTTAAAGATTGTTGATCTCTCAGCGgtatgctctg ... ttgcttacagGACTTCCGACTACGCGACATCAATGAGTATGCTGAGTGGTATGGACATTCC
EST: gi|148946776|gb|EC892045.2|EC892045
EST:     AAATTATCAAAAGCTTACCCCGACACTTAAAGATTGTTGATCTCTCAGCG                         GACTTCCGACTACGCGACATCAATGAGTATGCTGAGTGGTATGGACATTCC
genomic: AAATTATCAAAAGCTTACCCCGACACTTAAAGATTGTTGATCTCTCAGCGgtatgctctg ... ttgcttacagGACTTCCGACTACGCGACATCAATGAGTATGCTGAGTGGTATGGACATTCC
EST: gi|89757643|gb|DY687157.1|DY687157
EST:     AAATTATCAAAAGCTTACCCCGACACTTAAAGATTGTTGATCTCTCAGCG                         GACTTCCGACTACGCGACATCAATGAGTATGCTGAGTGGTATGGACATTCC
genomic: AAATTATCAAAAGCTTACCCCGACACTTAAAGATTGTTGATCTCTCAGCGgtatgctctg ... ttgcttacagGACTTCCGACTACGCGACATCAATGAGTATGCTGAGTGGTATGGACATTCC
EST: gi|148942779|gb|EC887806.2|EC887806
EST:     AAATTATCAAAAGCTTACCCCGACACTTAAAGATTGTTGATCTCTCAGCG                         GACTTCCGACTACCCGACATCAATGAGTATGCTGAGTGGTATGGACATTCC
genomic: AAATTATCAAAAGCTTACCCCGACACTTAAAGATTGTTGATCTCTCAGCGgtatgctctg ... ttgcttacagGACTTCCGACTACGCGACATCAATGAGTATGCTGAGTGGTATGGACATTCC
EST: gi|71429367|gb|DR810417.1|DR810417
EST:     AAATTATCAAAAGCTTACCCCGACACTTAAAGATTGTTGATCTCTCAGCG                         GACTTCCGACTACGCGACATCAATGAGTATGCTGAGTGGTATGGACATTCC
genomic: AAATTATCAAAAGCTTACCCCGACACTTAAAGATTGTTGATCTCTCAGCGgtatgctctg ... ttgcttacagGACTTCCGACTACGCGACATCAATGAGTATGCTGAGTGGTATGGACATTCC
EST: gi|91878697|gb|EB408654.1|EB408654
EST:     TTATCAAAAGCTTACCCCCCGACACCTTAAAGATTGTTGATCTCTCAGCG                         GATTTCCGACTACCCCGACATCAATGAGTATGCTGAGTGGTAT
genomic: TTATCAAAAGCTTACCCC--GACAC-TTAAAGATTGTTGATCTCTCAGCGgtatgctctg ... ttgcttacagGACTTCCGACTACGC-GACATCAATGAGTATGCTGAGTGGTAT
EST: gi|148946555|gb|EC884293.2|EC884293
EST:     AAATTATCAAAAGCTTACCCCGACACTTAAAGATTGTTGATCTCTCAGCG                         GACTTCCGACTACGCGACATCAATGAGTATG
genomic: AAATTATCAAAAGCTTACCCCGACACTTAAAGATTGTTGATCTCTCAGCGgtatgctctg ... ttgcttacagGACTTCCGACTACGCGACATCAATGAGTATG
EST: gi|78080160|gb|DV508572.1|DV508572
EST:     AAATTATCAAAAGCTTACCCCGACACTTAAAGATTGTTGATCTCTCAGCG                         GACTTCCGACTACGCGACATCAATGAGTATGCTGAGTGGTATGGACATTCC
genomic: AAATTATCAAAAGCTTACCCCGACACTTAAAGATTGTTGATCTCTCAGCGgtatgctctg ... ttgcttacagGACTTCCGACTACGCGACATCAATGAGTATGCTGAGTGGTATGGACATTCC
EST: gi|78079274|gb|DV507686.1|DV507686
EST:     AAATTATCAAAAGCTTACCCCGACACTTAAAGATTGTTGATCTCTCAGCG                         GACTTCCGACTACGCGACATCAATGAGTATGCTGAGTGGTATGGACATTCC
genomic: AAATTATCAAAAGCTTACCCCGACACTTAAAGATTGTTGATCTCTCAGCGgtatgctctg ... ttgcttacagGACTTCCGACTACGCGACATCAATGAGTATGCTGAGTGGTATGGACATTCC
EST: gi|74234671|gb|DT642585.1|DT642585
EST:     AAATTATCAAAAGCTTACCCCGACACTTAAAGATTGTTGATCTCTCAGCG                         GACTTCCGACTACGCGACATCAATGAGTATGCTGAGTGGTATGGACATTCC
genomic: AAATTATCAAAAGCTTACCCCGACACTTAAAGATTGTTGATCTCTCAGCGgtatgctctg ... ttgcttacagGACTTCCGACTACGCGACATCAATGAGTATGCTGAGTGGTATGGACATTCC
EST: gi|149074521|gb|EE162917.2|EE162917
EST:     AAATTATCAAAAGCTTACCCCGACACTTAAAGATTGTTGATCTCTCAGCG                         GACTTCCGACTACGCGACATCAATGAGTATGCTGAGTGGTATGGACATTCC
genomic: AAATTATCAAAAGCTTACCCCGACACTTAAAGATTGTTGATCTCTCAGCGgtatgctctg ... ttgcttacagGACTTCCGACTACGCGACATCAATGAGTATGCTGAGTGGTATGGACATTCC

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: 45 (upstream exon), 47 (downstream exon)
Score: 240

GAAATTATCAAAAGCTTACCCCGACACTTAAAGATTGTTGATCTCTCAGCGgtatgctctg ... ttgcttacagGACTTCCGACTACGCGACATCAATGAGTATGCTGAGTGGTATGGACATTCCCACAGGGCACCGGAACTTCAG


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

GAAATTATCAAAAGCTTACCCCGACACTTAAAGATTGTTGATCTCTCAGCGgtatgctctg ... ttgcttacagGACTTCCGACTACGCGACATCAATGAGTATGCTGAGTGGTATGGACATTCCCACAGGGCACCGGAACTTCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 181

GAAATTATCAAAAGCTTACCCCGACACTTAAAGATTGTTGATCTCTCAGCGgtatgctctg ... ttgcttacagGACTTCCGACTACGCGACATCAATGAGTATGCTGAGTGGTATGGACATTCCCACAGGGCACCGGAACTTCAG


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 146

GAAATTATCAAAAGCTTACCCCGACACTTAAAGATTGTTGATCTCTCAGCGgtatgctctg ... ttgcttacagGACTTCCGACTACGCGACATCAATGAGTATGCTGAGTGGTATGGACATTCCCACAGGGCACCGGAACTTCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actctatttacttctctaagtacgatctcagttgttgaaaaactattgcttacagGACTTCCGACTACGCGACATCAATGAGTATGCTGAGTGGTATGGACATTCCCACAGGGCACCGGAACTTCAG
                                     aaaaactatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgctctgcagtctgcacacactctatttacttctctaagtacgatctcagttgttgaaaaactattgcttacagGACTTCCGACTACGCGACATCAATGAGTATGCTGAGTGGTATGGACATTCCCACAGGGCACCGGAACTTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG