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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagacattttcagcagctggcatttctaattctatttgtttttctgcactgattttcacatggttccatgtgcaaataatagatacttgggattagagactgtcaggctgcttgttgatagtggttgcctgtagttttactaatcaaagcacttgtaatatttatgcagAAATTGGAAGAACTTGAAAAACGTCTACTGGATTTGGACACAGGTGCTGAGTCTGCAGTCCGAGCTGTTATTGAAGAATTTTCAACAGATGTTCAAACTG

Basic information

species Zea mays
transcript GRMZM2G042818_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G042818_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os01g54860.1 (Oryza sativa), 3'ss of exon 8
gtaagacattttcagcagctggcatttctaattctatttgtttttctgcactgattttcac-atggttccatgtgcaaataatagatacttgggattagagactgtcaggctgcttgttgatag--tggttgcctgtagttttactaatcaaag-cacttgtaatatttatg-cagAAATTGGAAGAACTTGAAAAACGTCTACTGGATTTGGACACAGGTGCTGAGTCTGCAGTCCGAGCTGTTATTGAAGAATTTTCAACAGATGTTCAAACTG
||||| ||||  |||||  |  ||||  || |     | |||    |||| |||||| | | || |||| |  || |           || |  |          |||   || |||||||||   ||  |  |||| |||  ||||| ||||     || |||| |  ||| |||||||||||||||||||||||| | || ||| ||||  ||||||| | ||||||||| || ||||||| ||||||||| || ||||| ||||||||| |||
gtaaggcatt--cagcatttaccattcatattcacgatggttccggtgca-tgatttcctcgattgttctacatgtag----------ctcgacaa--------atcaaaatgtttgttgatatattgtctttctgtggttggactaaccaaaaatgattataatgtgaatggcagAAATTGGAAGAACTTGAAAAATGCCTGCTGAATTTAAACACAGGAGATGAGTCTGCTGTTCGAGCTGCTATTGAAGAGTTCTCAACTGATGTTCAACCTG
















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|33942681|gb|CF349281.1|CF349281
EST:     CGAAGGAAATGATTTCTGCTGGTCTTGCTACTCATTTTGTCAGTTCTGAA                         AAATTGGAAGAACTTGAAAAAACGTCTACTGGATTTGGACACAGGTGCTGA
genomic: CGAAGGAAATGATTTCTGCTGGTCTTGCTACTCATTTTGTCAGTTCTGAAgtaagacatt ... atttatgcagAAATTGGAAGAACTTGAAAAA-CGTCTACTGGATTTGGACACAGGTGCTGA
EST: gi|101390789|gb|EB817329.1|EB817329
EST:     CGAAGGAAATGATTTCTGCTGGTCTTGCTACTCATTTTGTCAGTTCTGAA                         AAATTGGAAGAACTTGAAAAACGTCTACTGGATTTGGACACAGGTGCTGAG
genomic: CGAAGGAAATGATTTCTGCTGGTCTTGCTACTCATTTTGTCAGTTCTGAAgtaagacatt ... atttatgcagAAATTGGAAGAACTTGAAAAACGTCTACTGGATTTGGACACAGGTGCTGAG
EST: gi|71448792|gb|DR829842.1|DR829842
EST:     CGAAGGAAATGATTTCTGCTGGTCTTGCTACTCATTTTGTCAGTTCTGAA                         AAATTGAAAGAACTTGAAAAACGTCTACT
genomic: CGAAGGAAATGATTTCTGCTGGTCTTGCTACTCATTTTGTCAGTTCTGAAgtaagacatt ... atttatgcagAAATTGGAAGAACTTGAAAAACGTCTACT
EST: gi|37400624|gb|CF637668.1|CF637668
EST:     CGAAGGAAATGATTTCTGCTGGTCTTGCTACTCATTTTGTCAGTTCTGAA                         AAATTGGAAGAACTTGAAAAACGTCTACTGGATTTGGACACAGGTGCTGAG
genomic: CGAAGGAAATGATTTCTGCTGGTCTTGCTACTCATTTTGTCAGTTCTGAAgtaagacatt ... atttatgcagAAATTGGAAGAACTTGAAAAACGTCTACTGGATTTGGACACAGGTGCTGAG
EST: gi|78109535|gb|DV527951.1|DV527951
EST:     CGAAGGAAATGATTTCTGCTGGTCTTGCTACTCATTTTGTCAGTTCTGAA                         AAATTGGAAGAACTTGAAAAACGTCTACTGGATTTGGACACAGGTGCTGAG
genomic: CGAAGGAAATGATTTCTGCTGGTCTTGCTACTCATTTTGTCAGTTCTGAAgtaagacatt ... atttatgcagAAATTGGAAGAACTTGAAAAACGTCTACTGGATTTGGACACAGGTGCTGAG
EST: gi|15177481|gb|BI398420.1|BI398420
EST:     CGAAGGAAATGATTTCTGCTGGTCTTGCTACTCATTTTGTCAGTTCTGAA                         AAA-TGGAAGAACTTGAAAAACGTCTACTGGATTTGGACACAGGTGCTGAG
genomic: CGAAGGAAATGATTTCTGCTGGTCTTGCTACTCATTTTGTCAGTTCTGAAgtaagacatt ... atttatgcagAAATTGGAAGAACTTGAAAAACGTCTACTGGATTTGGACACAGGTGCTGAG
EST: gi|149000045|gb|EE037146.2|EE037146
EST:     CGAAGGAAATGATTTCTGCTGGTCTTGCTACTCATTTTGTCAGTTCTGAA                         AAATTGGAAGAACTTGAAAAACGTCTACTGGATTTGGACACAGGTGCTGAG
genomic: CGAAGGAAATGATTTCTGCTGGTCTTGCTACTCATTTTGTCAGTTCTGAAgtaagacatt ... atttatgcagAAATTGGAAGAACTTGAAAAACGTCTACTGGATTTGGACACAGGTGCTGAG
EST: gi|74239820|gb|DT647734.1|DT647734
EST:     CGAAGGAAATGATTTCTGCTGGTCTTGCTACTCATTTTGTCAGTTCTGAA                         AAATTTGGA-GAACTTGAAAAACGTCTAC
genomic: CGAAGGAAATGATTTCTGCTGGTCTTGCTACTCATTTTGTCAGTTCTGAAgtaagacatt ... atttatgcagAAATT-GGAAGAACTTGAAAAACGTCTAC
EST: gi|71304196|gb|DR788218.1|DR788218
EST:     CGAAGGAAATGATTTCTGCTGGTCTTGCTACTCATTTTGTCAGTTCTGAA                         AAATTGGAAGAACTTGAAAAACGTCTACTGGATTTGGACACAGGTGCTGAG
genomic: CGAAGGAAATGATTTCTGCTGGTCTTGCTACTCATTTTGTCAGTTCTGAAgtaagacatt ... atttatgcagAAATTGGAAGAACTTGAAAAACGTCTACTGGATTTGGACACAGGTGCTGAG
EST: gi|60352184|gb|DN219157.1|DN219157
EST:     CGAAGGAAATGATTTCTGCTGGTCTTGCTACTCATTTTGTCAGTTCTGAA                         AAATTGGAAGAACTTGAAAAACGTCTACTGGATTTGGACACAGGTGCTGAG
genomic: CGAAGGAAATGATTTCTGCTGGTCTTGCTACTCATTTTGTCAGTTCTGAAgtaagacatt ... atttatgcagAAATTGGAAGAACTTGAAAAACGTCTACTGGATTTGGACACAGGTGCTGAG
EST: gi|30052459|gb|AI065748.2|AI065748
EST:     CGAAGGAAATGATTTCTGCTGGTCTTGCTACTCATTTTGTCAGTTCTGAA                         AAATTGGAAGAACTTGAAAAACGTCTACTGGATTTGGACACAGGTGCTGAG
genomic: CGAAGGAAATGATTTCTGCTGGTCTTGCTACTCATTTTGTCAGTTCTGAAgtaagacatt ... atttatgcagAAATTGGAAGAACTTGAAAAACGTCTACTGGATTTGGACACAGGTGCTGAG
EST: gi|32930057|gb|CF034869.1|CF034869
EST:     CGAAGGAAATGATTTCTGCTGGTCTTGCTACTCATTTTGTCAGTTCTGAA                         AAATTGGAAGAACTTGAAAAACGTCTACTGGATTTGGACACAGGTGCTGAG
genomic: CGAAGGAAATGATTTCTGCTGGTCTTGCTACTCATTTTGTCAGTTCTGAAgtaagacatt ... atttatgcagAAATTGGAAGAACTTGAAAAACGTCTACTGGATTTGGACACAGGTGCTGAG
EST: gi|93012152|gb|EB637672.1|EB637672
EST:     CGAAGGAAATGATTTCTGCTGGTCTTGCTACTCATTTTGTCAGTTCTGAA                         AAATTTGGAAGAACTTGAAAAACGTCTACTGGATTTGGACACAGGTGCTGA
genomic: CGAAGGAAATGATTTCTGCTGGTCTTGCTACTCATTTTGTCAGTTCTGAAgtaagacatt ... atttatgcagAAATT-GGAAGAACTTGAAAAACGTCTACTGGATTTGGACACAGGTGCTGA
EST: gi|91056953|gb|EB167371.1|EB167371
EST:     CGAAGGAAATGATTTCTGCTGGTCTTGCTACTCATTTTGTCAGTTCTGAA                         AAATTGAAAGAACTTGAAAAACGTCTACTGGATTTGGACACAGGTGCTGAG
genomic: CGAAGGAAATGATTTCTGCTGGTCTTGCTACTCATTTTGTCAGTTCTGAAgtaagacatt ... atttatgcagAAATTGGAAGAACTTGAAAAACGTCTACTGGATTTGGACACAGGTGCTGAG
EST: gi|40303747|gb|CK348134.1|CK348134
EST:     CGAAGGAAATGATTTCTGCTGGTCTTGCTACTCATTTTGTCAGTTCTGAA                         AAA-TGGAANGAACTTGAAAAACGTCTACTGGATTTGGACACAGGTGCTGA
genomic: CGAAGGAAATGATTTCTGCTGGTCTTGCTACTCATTTTGTCAGTTCTGAAgtaagacatt ... atttatgcagAAATTGGAA-GAACTTGAAAAACGTCTACTGGATTTGGACACAGGTGCTGA
EST: gi|149089063|gb|EE178226.2|EE178226
EST:     CGAAGGAAATGATTTCTGCTGGTCTTGCTACTCATTTTGTCAGTTCTGAA                         AAATTGGAAGAACTTGAAAAACGTCTACTGGATTTGGACACAGGTGCTGAG
genomic: CGAAGGAAATGATTTCTGCTGGTCTTGCTACTCATTTTGTCAGTTCTGAAgtaagacatt ... atttatgcagAAATTGGAAGAACTTGAAAAACGTCTACTGGATTTGGACACAGGTGCTGAG
EST: gi|148959115|gb|EE010592.2|EE010592
EST:     CGAAGGAAATGATTTCTGCTGGTCTTGCTACTCATTTTGTCAGTTCTGAA                         AAATTGGAAGAACTTGAAAAACGTCTACTGGATTTGGACACAGGTGCTGAG
genomic: CGAAGGAAATGATTTCTGCTGGTCTTGCTACTCATTTTGTCAGTTCTGAAgtaagacatt ... atttatgcagAAATTGGAAGAACTTGAAAAACGTCTACTGGATTTGGACACAGGTGCTGAG
EST: gi|74238393|gb|DT646307.1|DT646307
EST:     CGAAGGAAATGATTTCTGCTGGTCTTGCTACTCATTTTGTCAGTTCTGAA                         AAATTGGAAGAAACTTGAAAA-CGTCTACTGGATTTGGACACAGGTGCTGA
genomic: CGAAGGAAATGATTTCTGCTGGTCTTGCTACTCATTTTGTCAGTTCTGAAgtaagacatt ... atttatgcagAAATTGGAAGAA-CTTGAAAAACGTCTACTGGATTTGGACACAGGTGCTGA
EST: gi|71447954|gb|DR829004.1|DR829004
EST:     CGAAGGAAATGATTTCTGCTGGTCTTGCTACTCATTTTGTCAGTTCTGAA                         AAATTGAAAGAACTTGAAAA-CGTCTACTGGATTTGGACACAGGTGCTGAG
genomic: CGAAGGAAATGATTTCTGCTGGTCTTGCTACTCATTTTGTCAGTTCTGAAgtaagacatt ... atttatgcagAAATTGGAAGAACTTGAAAAACGTCTACTGGATTTGGACACAGGTGCTGAG

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: 49 (upstream exon), 49 (downstream exon)
Score: 88

GCGAGTATCTGGCTTTAACTGGTGCTAGACTGAATGCGAAGGAAATGATTTCTGCTGGTCTTGCTACTCATTTTGTCAGTTCTGAAgtaagacatt ... atttatgcagAAATTGGAAGAACTTGAAAAACGTCTACTGGATTTGGACACAGGTGCTGAGTCTGCAGTCCGAGCTGTTATTGAAGAATTTTCAACAGATGTTCAAACTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 257

GCGAGTATCTGGCTTTAACTGGTGCTAGACTGAATGCGAAGGAAATGATTTCTGCTGGTCTTGCTACTCATTTTGTCAGTTCTGAAgtaagacatt ... atttatgcagAAATTGGAAGAACTTGAAAAACGTCTACTGGATTTGGACACAGGTGCTGAGTCTGCAGTCCGAGCTGTTATTGAAGAATTTTCAACAGATGTTCAAACTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 234

GCGAGTATCTGGCTTTAACTGGTGCTAGACTGAATGCGAAGGAAATGATTTCTGCTGGTCTTGCTACTCATTTTGTCAGTTCTGAAgtaagacatt ... atttatgcagAAATTGGAAGAACTTGAAAAACGTCTACTGGATTTGGACACAGGTGCTGAGTCTGCAGTCCGAGCTGTTATTGAAGAATTTTCAACAGATGTTCAAACTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 244

GCGAGTATCTGGCTTTAACTGGTGCTAGACTGAATGCGAAGGAAATGATTTCTGCTGGTCTTGCTACTCATTTTGTCAGTTCTGAAgtaagacatt ... atttatgcagAAATTGGAAGAACTTGAAAAACGTCTACTGGATTTGGACACAGGTGCTGAGTCTGCAGTCCGAGCTGTTATTGAAGAATTTTCAACAGATGTTCAAACTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgatagtggttgcctgtagttttactaatcaaagcacttgtaatatttatgcagAAATTGGAAGAACTTGAAAAACGTCTACTGGATTTGGACACAGGTGCTGAGTCTGCAGTCCGAGCTGTTATTGAAGAATTTTCAACAGATGTTCAAACTG
                       tactaat  putative branch site (score: 244)
                                    acttgtaatatttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagacattttcagcagctggcatttctaattctatttgtttttctgcactgattttcacatggttccatgtgcaaataatagatacttgggattagagactgtcaggctgcttgttgatagtggttgcctgtagttttactaatcaaagcacttgtaatatttatgcagAAATTGGAAGAACTTGAAAAACGTCTACTGGATTTGGACACAGGTGCTGAGTCTGCAGTCCGAGCTGTTATTGAAGAATTTTCAACAGATGTTCAAACTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG