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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCGTACATCAAGCAGCTGCAGCAGAAGGTGGTGAGGCTGAACCAGGAGATTGCCTGCGCGCAGGACGCCCTGAGACACAAGTCCTCCTCCTATCCGACGgtatatataatctcatcgcatatgcagattttgccacacgtagagagaccgacagcgtgttgttgattgacgatgaaataaacgggccggccgtcggcggatatgtatatgctatggatgcag

Basic information

species Zea mays
transcript GRMZM2G124567_T02
intron # 2
splice site 5'
intron type U2

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|74246352|gb|DT654266.1|DT654266
EST:     TTGCCTGCGCGCAGGACGCCCTGAGACACAAGTCCTCCTCCTATCCGACG                         GTGACCGTGGAAACCCTAGGAGTGCAGGGGTTCCTCGTCAACGTGTTCTCC
genomic: TTGCCTGCGCGCAGGACGCCCTGAGACACAAGTCCTCCTCCTATCCGACGgtatatataa ... atggatgcagGTGACCGTGGAAACCCTAGGAGTGCAGGGGTTCCTCGTCAACGTGTTCTCC
EST: gi|211389355|gb|FL471371.1|FL471371
EST:     TTGCCTGCGCGCAGGACGCCCTGAGACACAAGTCCTCCTCCTATCCGACG                         GTGACCGTGGAAACCCTAGGAGTGCAGGGGTTCCTCGTCAACGTGTTCTCC
genomic: TTGCCTGCGCGCAGGACGCCCTGAGACACAAGTCCTCCTCCTATCCGACGgtatatataa ... atggatgcagGTGACCGTGGAAACCCTAGGAGTGCAGGGGTTCCTCGTCAACGTGTTCTCC
EST: gi|211446503|gb|FK979162.1|FK979162
EST:     TTGCCTGCGCGCAGGACGCCCTGAGACACAAGTCCTCCTCCTATCCGACG                         GTGACCGTGGAAACCCTAGGAGTGC
genomic: TTGCCTGCGCGCAGGACGCCCTGAGACACAAGTCCTCCTCCTATCCGACGgtatatataa ... atggatgcagGTGACCGTGGAAACCCTAGGAGTGC
EST: gi|60400731|gb|DN233538.1|DN233538
EST:     TTGCCTGCGCGCAGGACGCCCTGAGACACAAGTCCTCCTCCTATCCGACG                         GTGACCGTGGAAACCCTAGGAGTGCAGGGGTTCCTCGTCAACGTGTTCTCC
genomic: TTGCCTGCGCGCAGGACGCCCTGAGACACAAGTCCTCCTCCTATCCGACGgtatatataa ... atggatgcagGTGACCGTGGAAACCCTAGGAGTGCAGGGGTTCCTCGTCAACGTGTTCTCC
EST: gi|211446497|gb|FK979156.1|FK979156
EST:     TTGCCTGCGCGCAGGACGCCCTGAGACACAAGTCCTCCTCCTATCCGACG                         GTGACCGTGGAAACCCTAGGAGTGCAGGGGTTCCTCGTCAACGTGTTCTCC
genomic: TTGCCTGCGCGCAGGACGCCCTGAGACACAAGTCCTCCTCCTATCCGACGgtatatataa ... atggatgcagGTGACCGTGGAAACCCTAGGAGTGCAGGGGTTCCTCGTCAACGTGTTCTCC
EST: gi|211446499|gb|FK979158.1|FK979158
EST:     TTGCCTGCGCGCAGGACGCCCTGAGACACAAGTCCTCCTCCTATCCGACG                         GTGACCGTGGAAACCCT
genomic: TTGCCTGCGCGCAGGACGCCCTGAGACACAAGTCCTCCTCCTATCCGACGgtatatataa ... atggatgcagGTGACCGTGGAAACCCT
EST: gi|76293000|gb|DV032568.1|DV032568
EST:     TTGCCTGCGCGCAGGACGCCCTGAGACACAAGTCCTCCTCCTATCCGACG                         GTGACCGTGGAAACCCTAGGAGTGCAGGGGTTCCTCGTCAACGTGTTCTCC
genomic: TTGCCTGCGCGCAGGACGCCCTGAGACACAAGTCCTCCTCCTATCCGACGgtatatataa ... atggatgcagGTGACCGTGGAAACCCTAGGAGTGCAGGGGTTCCTCGTCAACGTGTTCTCC
EST: gi|211446493|gb|FK979152.1|FK979152
EST:     TTGCCTGCGCGCAGGACGCCCTGAGACACAAGTCCTCCTCCTATCCGACG                         GTGACCGTGGAAACCCTAGGA
genomic: TTGCCTGCGCGCAGGACGCCCTGAGACACAAGTCCTCCTCCTATCCGACGgtatatataa ... atggatgcagGTGACCGTGGAAACCCTAGGA
EST: gi|78087747|gb|DV516140.1|DV516140
EST:     TTGCCTGCGCGCAGGACGCCCTGAGACACAAGTCCTCCTCCTATCCGACG                         GTGACCGTGGAAACCCTAGGAGTGCAGGGGTTCCTCGTCAACGTGTTCTCC
genomic: TTGCCTGCGCGCAGGACGCCCTGAGACACAAGTCCTCCTCCTATCCGACGgtatatataa ... atggatgcagGTGACCGTGGAAACCCTAGGAGTGCAGGGGTTCCTCGTCAACGTGTTCTCC
EST: gi|16916338|gb|BM072801.1|BM072801
EST:     TTGCTTGCGCGCAGGACGCCCTGAGACACAAGTCCTCCTCCTATCCGACG                         GTGACCGTGGAAACCCTAGGAGTGCAGGGGTTCCTCGTCAACGTGTTCTCC
genomic: TTGCCTGCGCGCAGGACGCCCTGAGACACAAGTCCTCCTCCTATCCGACGgtatatataa ... atggatgcagGTGACCGTGGAAACCCTAGGAGTGCAGGGGTTCCTCGTCAACGTGTTCTCC
EST: gi|211446502|gb|FK979161.1|FK979161
EST:     TTGCCTGCGCGCAGGACGCCCTGAGACACAAGTCCTCCTCCTATCCGACG                         GTGACCGTGGAAACCCTAGGAGTGCAGGGGTTCCTCGTCAACGTGTTCTCC
genomic: TTGCCTGCGCGCAGGACGCCCTGAGACACAAGTCCTCCTCCTATCCGACGgtatatataa ... atggatgcagGTGACCGTGGAAACCCTAGGAGTGCAGGGGTTCCTCGTCAACGTGTTCTCC
EST: gi|78087746|gb|DV516139.1|DV516139
EST:     TTGCCTGCGCGCAGGACGCCCTGAGACACAAGTCCTCCTCCTATCCGACG                         GTGACCGTGGAAACCCTAGGAGTGCAGGGGTTCCTCGTCAACGTGTTCTCC
genomic: TTGCCTGCGCGCAGGACGCCCTGAGACACAAGTCCTCCTCCTATCCGACGgtatatataa ... atggatgcagGTGACCGTGGAAACCCTAGGAGTGCAGGGGTTCCTCGTCAACGTGTTCTCC
EST: gi|211446501|gb|FK979160.1|FK979160
EST:     TTGCCTGCGCGCAGGACGCCCTGAGACACAAGTCCTCCTCCTATCCGACG                         GTGACCGTGGAAACCCTAGGAG
genomic: TTGCCTGCGCGCAGGACGCCCTGAGACACAAGTCCTCCTCCTATCCGACGgtatatataa ... atggatgcagGTGACCGTGGAAACCCTAGGAG
EST: gi|211446498|gb|FK979157.1|FK979157
EST:     TTGCCTGCGCGCAGGACGCCCTGAGACACAAGTCCTCCTCCTATCCGACG                         GTGACCGTGGAAACCCTAGGAGTGCAGGGGTTCCTCGTCAACGTGTTCTCC
genomic: TTGCCTGCGCGCAGGACGCCCTGAGACACAAGTCCTCCTCCTATCCGACGgtatatataa ... atggatgcagGTGACCGTGGAAACCCTAGGAGTGCAGGGGTTCCTCGTCAACGTGTTCTCC
EST: gi|71306652|gb|DR789486.1|DR789486
EST:     TTGCCTGCGCGCAGGACGCCCTGAGACACAAGTCCTCCTCCTATCCGACG                         GTGACCGTGGAAACCCTAGGAGTGCAGGGGTTCCTCGTCAACGTGTTCTCC
genomic: TTGCCTGCGCGCAGGACGCCCTGAGACACAAGTCCTCCTCCTATCCGACGgtatatataa ... atggatgcagGTGACCGTGGAAACCCTAGGAGTGCAGGGGTTCCTCGTCAACGTGTTCTCC
EST: gi|71306651|gb|DR789485.1|DR789485
EST:     TTGCCTGCGCGCAGGACGCCCTGAGACACAAGTCCTCCTCCTATCCGACG                         GTGACCGTGGAAACCCTAGGAGTGCAGGGGTTCCTCGTCAACGTGTTCTCC
genomic: TTGCCTGCGCGCAGGACGCCCTGAGACACAAGTCCTCCTCCTATCCGACGgtatatataa ... atggatgcagGTGACCGTGGAAACCCTAGGAGTGCAGGGGTTCCTCGTCAACGTGTTCTCC
EST: gi|211446500|gb|FK979159.1|FK979159
EST:     TTGCCTGCGCGCAGGACGCCCTGAGACACAAGTCCTCCTCCTATCCGACG                         GTGACCGTGGAAACCCTAGGAGTGCAGGGGTTCCTCGTCAACGTGTTCTCC
genomic: TTGCCTGCGCGCAGGACGCCCTGAGACACAAGTCCTCCTCCTATCCGACGgtatatataa ... atggatgcagGTGACCGTGGAAACCCTAGGAGTGCAGGGGTTCCTCGTCAACGTGTTCTCC
EST: gi|76015156|gb|DT942326.1|DT942326
EST:     TTGCCTGCGCGCAGGACGCCCTGAGACACAAGTCCTCCTCCTATCCGACG                         GTGACCGTGGAAACCCTAGGAGTGCAGGGGTTCCTCGTCAACGTGTTCTCC
genomic: TTGCCTGCGCGCAGGACGCCCTGAGACACAAGTCCTCCTCCTATCCGACGgtatatataa ... atggatgcagGTGACCGTGGAAACCCTAGGAGTGCAGGGGTTCCTCGTCAACGTGTTCTCC

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 2 RNA-Seq libraries.


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 26

GGCGTACATCAAGCAGCTGCAGCAGAAGGTGGTGAGGCTGAACCAGGAGATTGCCTGCGCGCAGGACGCCCTGAGACACAAGTCCTCCTCCTATCCGACGgtatatataa ... atggatgcagGTGACCGTGGAAACCCTAGGAGTGCAGGGGTTCCTCGTCAACGTGTTCTCCGACAAGAGCTGCCCGGGGCTGCTCGTCTCCGTCCTGGAAGCCTTCGACG


Block sizes: 48 (upstream exon), 43 (downstream exon)
Score: 8

GGCGTACATCAAGCAGCTGCAGCAGAAGGTGGTGAGGCTGAACCAGGAGATTGCCTGCGCGCAGGACGCCCTGAGACACAAGTCCTCCTCCTATCCGACGgtatatataa ... atggatgcagGTGACCGTGGAAACCCTAGGAGTGCAGGGGTTCCTCGTCAACGTGTTCTCCGACAAGAGCTGCCCGGGGCTGCTCGTCTCCGTCCTGGAAGCCTTCGACG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCGTACATCAAGCAGCTGCAGCAGAAGGTGGTGAGGCTGAACCAGGAGATTGCCTGCGCGCAGGACGCCCTGAGACACAAGTCCTCCTCCTATCCGACGgtatatataatctcatcgcatatgcagattttgccacacgtagagagaccgacagcgtgttgttgattgacgatgaaataaacgggccggccgtcggcggatatgtatatgctatggatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC