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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttctattccacgaaattgtagaaaatttcatgttttgctctgatgcattctttgttcagtatcacattcagtgttgtgatatgtaacttggacactgcagAAATGGAAAGATGCAGATGGAGGAGACAGACACAGATGATAGCAACTCGTTTGTCACTTCTGTAAAAGCAAAAGCAAAACGTGTACTGTTGAAGGCAAAG

Basic information

species Zea mays
transcript GRMZM2G144254_T06
intron # 11
splice site 3'
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|60359035|gb|DN226008.1|DN226008
EST:     ACGAAAGATGGTTCGAGCACTGCCGAGGAATCTATAATTGATATGGACAG                         AAATGGAAAGATGCAGATGGAGGAGACAGACACAGATGATAGCAACTCGTT
genomic: ACGAAAGATGGTTCGAGCACTGCCGAGGAATCTATAATTGATATGGACAGgttctattcc ... gacactgcagAAATGGAAAGATGCAGATGGAGGAGACAGACACAGATGATAGCAACTCGTT
EST: gi|88756245|gb|DY540386.1|DY540386
EST:     TTCGAGCACTGCCGGGGAATTTATAATTGATATGGACAG                         AAATGGAAAGATGCAGATGGAGGAGACAGACACAGATGATAGCAACTCGTT
genomic: TTCGAGCACTGCCGAGGAATCTATAATTGATATGGACAGgttctattcc ... gacactgcagAAATGGAAAGATGCAGATGGAGGAGACAGACACAGATGATAGCAACTCGTT
EST: gi|93281607|gb|EB673871.1|EB673871
EST:     ACGAAAGATGGTTCGAGCACTGCCGAGGAATCTATAATTGATATGGACAG                         AAATGGAAAGATGCAGATGGAGGAGACAGACACAGATGATAGCAACTCGTT
genomic: ACGAAAGATGGTTCGAGCACTGCCGAGGAATCTATAATTGATATGGACAGgttctattcc ... gacactgcagAAATGGAAAGATGCAGATGGAGGAGACAGACACAGATGATAGCAACTCGTT
EST: gi|32844477|gb|CD984158.1|CD984158
EST:     ACGAAAGATGGTTCGAGCACTGCCGAGGAATCTATAATTGATATGGACAG                         AAATGGAAAGATGCAGATGGAGGAGACAGACACAGATGATAGCAACTCGTT
genomic: ACGAAAGATGGTTCGAGCACTGCCGAGGAATCTATAATTGATATGGACAGgttctattcc ... gacactgcagAAATGGAAAGATGCAGATGGAGGAGACAGACACAGATGATAGCAACTCGTT
EST: gi|5296213|gb|AI782893.1|AI782893
EST:     ACGAAAGATGGTTCGAGCACTGCCGAGGAATCTATAATTGATATGGACAG                         AAATGGAAAGATGCAGATGGAGGAGACAGACACAGATGATAGCAACTCGTT
genomic: ACGAAAGATGGTTCGAGCACTGCCGAGGAATCTATAATTGATATGGACAGgttctattcc ... gacactgcagAAATGGAAAGATGCAGATGGAGGAGACAGACACAGATGATAGCAACTCGTT
EST: gi|32808432|gb|CD960666.1|CD960666
EST:     ACGAAAGATGGTTCGAGCACTGCCGAGGAATCTATAATTGATATGGACAG                         AAATGGAAAGATGCAGATGGAGGAGACAGACACAGATGATAGCAACTCGTT
genomic: ACGAAAGATGGTTCGAGCACTGCCGAGGAATCTATAATTGATATGGACAGgttctattcc ... gacactgcagAAATGGAAAGATGCAGATGGAGGAGACAGACACAGATGATAGCAACTCGTT
EST: gi|88756206|gb|DY540347.1|DY540347
EST:     ATCTATAATTGATATGGACAG                         AAATGGAAAGATGCAGATGGAGGAGACAGACACAGATGATAGCAACTCGTT
genomic: ATCTATAATTGATATGGACAGgttctattcc ... gacactgcagAAATGGAAAGATGCAGATGGAGGAGACAGACACAGATGATAGCAACTCGTT
EST: gi|6828189|gb|AW331832.1|AW331832
EST:     ACGAAAGATGGTTCGAGCNCTGCCGAGGAATCTATAATTGATATGGACAG                         AAATGGAAAGATGCAGATGGAGGAGACAGACACAGATGATAGCAACTCGTT
genomic: ACGAAAGATGGTTCGAGCACTGCCGAGGAATCTATAATTGATATGGACAGgttctattcc ... gacactgcagAAATGGAAAGATGCAGATGGAGGAGACAGACACAGATGATAGCAACTCGTT
EST: gi|6227147|gb|AW155676.1|AW155676
EST:     ACGAAAGATGGTTCGAGCACTGCCGAGGAATCTATAATTGATATGGACAG                         AAATGGAAAGATGCAGATGGAGGAGACAGACACAGATGATAGCAACTCGTT
genomic: ACGAAAGATGGTTCGAGCACTGCCGAGGAATCTATAATTGATATGGACAGgttctattcc ... gacactgcagAAATGGAAAGATGCAGATGGAGGAGACAGACACAGATGATAGCAACTCGTT
EST: gi|32792658|gb|CD944894.1|CD944894
EST:     ACGAAAGATGGTTCGAGCACTGCCGAGGAATCTATAATTGATATGGACAG                         AAATGGAAAGATGCAGATGGAGGAGACAGACACAGATGATAGCAACTCGTT
genomic: ACGAAAGATGGTTCGAGCACTGCCGAGGAATCTATAATTGATATGGACAGgttctattcc ... gacactgcagAAATGGAAAGATGCAGATGGAGGAGACAGACACAGATGATAGCAACTCGTT
EST: gi|60351321|gb|DN218294.1|DN218294
EST:     ACGAAAGATGGTTCGAGCACTGCCGAGGAATCTATAATTGATATGGACAG                         AAATGGAAAGATGCAGATGGAGGAGACAGACACAGATGATAGCAACTCGTT
genomic: ACGAAAGATGGTTCGAGCACTGCCGAGGAATCTATAATTGATATGGACAGgttctattcc ... gacactgcagAAATGGAAAGATGCAGATGGAGGAGACAGACACAGATGATAGCAACTCGTT
EST: gi|113701592|gb|EE679096.1|EE679096
EST:     ACGAAAGATGGTTCGAGCACTGCCGAGGAATCTATAATTGATATGGACAG                         AAATGGAAAGATGCAGATGGAGGAGACAGACACAGATGATAGCAACTCGTT
genomic: ACGAAAGATGGTTCGAGCACTGCCGAGGAATCTATAATTGATATGGACAGgttctattcc ... gacactgcagAAATGGAAAGATGCAGATGGAGGAGACAGACACAGATGATAGCAACTCGTT
EST: gi|211277446|gb|FL309933.1|FL309933
EST:     ACGAAAGATGGTTCGAGCACTGCCGAGGAATCTATAATTGATATGGACAG                         AAATGGAAAGATGCAGATGGAGGAGACAGACACAGATGATAGCAACTCGTT
genomic: ACGAAAGATGGTTCGAGCACTGCCGAGGAATCTATAATTGATATGGACAGgttctattcc ... gacactgcagAAATGGAAAGATGCAGATGGAGGAGACAGACACAGATGATAGCAACTCGTT
EST: gi|60350817|gb|DN217790.1|DN217790
EST:     ACGAAAGATGGTTCGAGCACTGCCGAGGAATCTATAATTGATATGGACAG                         AAATGGAAAGATGCAGATGGAGGAGACAGACACAGATGATAGCAACTCGTT
genomic: ACGAAAGATGGTTCGAGCACTGCCGAGGAATCTATAATTGATATGGACAGgttctattcc ... gacactgcagAAATGGAAAGATGCAGATGGAGGAGACAGACACAGATGATAGCAACTCGTT
EST: gi|60356320|gb|DN223293.1|DN223293
EST:     ACGAAAGATGGTTCGAGCACTGCCGAGGAATCTATAATTGATATGGACAG                         AAATGGAAAGATGCAGATGGAGGAGACAGACACAGATGATAGCAACTCGTT
genomic: ACGAAAGATGGTTCGAGCACTGCCGAGGAATCTATAATTGATATGGACAGgttctattcc ... gacactgcagAAATGGAAAGATGCAGATGGAGGAGACAGACACAGATGATAGCAACTCGTT
EST: gi|19822362|gb|BQ048386.1|BQ048386
EST:     ACGAAAGATGGTTCGAGCACTGCCGAGGAATCTATAATTGATATGGACAG                         AAATGGAAAGATGCAGATGGAGGAGACAGACACAGATGATAGCAACTCGTT
genomic: ACGAAAGATGGTTCGAGCACTGCCGAGGAATCTATAATTGATATGGACAGgttctattcc ... gacactgcagAAATGGAAAGATGCAGATGGAGGAGACAGACACAGATGATAGCAACTCGTT
EST: gi|32844487|gb|CD984168.1|CD984168
EST:     ACGAAAGATGGTTCGAGCACTGCCGAGGAATCTATAATTGATATGGACAG                         AAATGGAAAGATGCAGATGGAGGAGACAGACACAGATGATAGCAACTCGTT
genomic: ACGAAAGATGGTTCGAGCACTGCCGAGGAATCTATAATTGATATGGACAGgttctattcc ... gacactgcagAAATGGAAAGATGCAGATGGAGGAGACAGACACAGATGATAGCAACTCGTT
EST: gi|5713925|gb|AI943910.1|AI943910
EST:     ACGAAAGATGGTTCGAGCCCTGCCGAGGAATCTATAATTGATATGGCCAG                         AAATGGAAAGATGCAGATGGAGGAGACAGACCCAGATGATAGCAACTCGTT
genomic: ACGAAAGATGGTTCGAGCACTGCCGAGGAATCTATAATTGATATGGACAGgttctattcc ... gacactgcagAAATGGAAAGATGCAGATGGAGGAGACAGACACAGATGATAGCAACTCGTT
EST: gi|19822356|gb|BQ048380.1|BQ048380
EST:     ACGAAAGATGGTTCGAGCACTGCCGAGGAATCTATAATTGATATGGACAG                         AAATGGAAAGATGCAGATGGAGGAGACAGACACAGATGATAGCAACTCGTT
genomic: ACGAAAGATGGTTCGAGCACTGCCGAGGAATCTATAATTGATATGGACAGgttctattcc ... gacactgcagAAATGGAAAGATGCAGATGGAGGAGACAGACACAGATGATAGCAACTCGTT
EST: gi|60399257|gb|DN232071.1|DN232071
EST:     AAGATGGTTCGAGCACTGCCGAGGAATCTATAATTGATATGGACAG                         AAATGGAAAGATGCAGATGGAGGAGACAGACACAGATGATAGCAACTCGTT
genomic: AAGATGGTTCGAGCACTGCCGAGGAATCTATAATTGATATGGACAGgttctattcc ... gacactgcagAAATGGAAAGATGCAGATGGAGGAGACAGACACAGATGATAGCAACTCGTT
EST: gi|78022546|gb|DV490933.1|DV490933
EST:     ACGAAAGATGGTTCGAGCACTGCCGAGGAATCTATAATTGATATGGACAG                         AAATGGAAAGATGCAGAT
genomic: ACGAAAGATGGTTCGAGCACTGCCGAGGAATCTATAATTGATATGGACAGgttctattcc ... gacactgcagAAATGGAAAGATGCAGAT

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), 48 (downstream exon)
Score: 139

CTGATACGAAAGATGGTTCGAGCACTGCCGAGGAATCTATAATTGATATGGACAGgttctattcc ... gacactgcagAAATGGAAAGATGCAGATGGAGGAGACAGACACAGATGATAGCAACTCGTTTGTCACTTCTGTAAAAGCAAAAGCAAAACGTGTACTGTTGAAGGCAAAG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 96

CTGATACGAAAGATGGTTCGAGCACTGCCGAGGAATCTATAATTGATATGGACAGgttctattcc ... gacactgcagAAATGGAAAGATGCAGATGGAGGAGACAGACACAGATGATAGCAACTCGTTTGTCACTTCTGTAAAAGCAAAAGCAAAACGTGTACTGTTGAAGGCAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 96

CTGATACGAAAGATGGTTCGAGCACTGCCGAGGAATCTATAATTGATATGGACAGgttctattcc ... gacactgcagAAATGGAAAGATGCAGATGGAGGAGACAGACACAGATGATAGCAACTCGTTTGTCACTTCTGTAAAAGCAAAAGCAAAACGTGTACTGTTGAAGGCAAAG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 131

CTGATACGAAAGATGGTTCGAGCACTGCCGAGGAATCTATAATTGATATGGACAGgttctattcc ... gacactgcagAAATGGAAAGATGCAGATGGAGGAGACAGACACAGATGATAGCAACTCGTTTGTCACTTCTGTAAAAGCAAAAGCAAAACGTGTACTGTTGAAGGCAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattctttgttcagtatcacattcagtgttgtgatatgtaacttggacactgcagAAATGGAAAGATGCAGATGGAGGAGACAGACACAGATGATAGCAACTCGTTTGTCACTTCTGTAAAAGCAAAAGCAAAACGTGTACTGTTGAAGGCAAAG
                                   atgtaac  putative branch site (score: 131)
                                 atatgtaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttctattccacgaaattgtagaaaatttcatgttttgctctgatgcattctttgttcagtatcacattcagtgttgtgatatgtaacttggacactgcagAAATGGAAAGATGCAGATGGAGGAGACAGACACAGATGATAGCAACTCGTTTGTCACTTCTGTAAAAGCAAAAGCAAAACGTGTACTGTTGAAGGCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG