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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgcacctcatttccaatgctgtagtaagtcatgtcttctgtgtgtatgtgtaaatgctgatgtattttattgctatcacagCTTCTCTACAGGAAGTACAGTGGAAACTTCCTTGTTAACCTTCTTGGGATGTGGAAGGAGTCTGAATACTCTGGCCATTCTGTTCCTGTTGGTGGTCTTG

Basic information

species Zea mays
transcript GRMZM2G073498_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G073498_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g11440.1 (Oryza sativa), 3'ss of exon 4
gtacgcacctcatttccaatgctgtagtaagtcatgtcttctgtgtgtatgtgtaaatgctgatgtattt-tattgctatcacagCTTCTCTACAGGAAGTACAGTGGAAACTTCCTTGTTAACCTTCTTGGGATGTGGAAGGAGTCTGAATACTCTGGCCATTCTGTTCCTGTTGGTGGTCTTG
||  | || ||| ||||| |||| ||| |||  |  ||||   ||| | ||| ||     | |  | ||| ||||||| |  |||||||||||||||| |||||||||||| ||||| || |||||| ||||||  |||||||| ||||| ||||||||||||||||||||||||||||||||||
gtctgaacttcaattccactgctttagcaagataaatctttaatgtttgtgtttag-cattaacatgtttgtattgctttggcagCTTCTCTACAGGAGGTACAGTGGAAATTTCCTAGTCAACCTTATTGGGAAATGGAAGGAATCTGAGTACTCTGGCCATTCTGTTCCTGTTGGTGGTCTTG
















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|32849493|gb|CD989174.1|CD989174
EST:     CCATCATTCTGCACTCTGCACTGATTACCAACCTCTATTTCATATCCCAG                         CTTCTCTACAGGAAGT
genomic: CCATCATTCTGCACTCTGCACTGATTACCAACCTCTATTTCATATCCCAGgtacgcacct ... gctatcacagCTTCTCTACAGGAAGT
EST: gi|6964762|gb|AW433455.1|AW433455
EST:     CCATCATTCTGCACTCTGCACTGATTACCAACCTCTATTTCATATCCCAG                         CTTCTCTACAGGAAGTAC
genomic: CCATCATTCTGCACTCTGCACTGATTACCAACCTCTATTTCATATCCCAGgtacgcacct ... gctatcacagCTTCTCTACAGGAAGTAC
EST: gi|32836577|gb|CD976255.1|CD976255
EST:     CCATCATTCTGCACTCTGCACTGATTACCAACCTCTATTTCATATCCCAG                         CTTCTCTACAGGAAGTA
genomic: CCATCATTCTGCACTCTGCACTGATTACCAACCTCTATTTCATATCCCAGgtacgcacct ... gctatcacagCTTCTCTACAGGAAGTA
EST: gi|32932204|gb|CF037016.1|CF037016
EST:     CCATCATTCTGCACTCTGCACTGATTACCAACCTCTATTTCATATCCCAG                         CTTCTCTACAGGAAGTA
genomic: CCATCATTCTGCACTCTGCACTGATTACCAACCTCTATTTCATATCCCAGgtacgcacct ... gctatcacagCTTCTCTACAGGAAGTA
EST: gi|211341222|gb|FL045918.1|FL045918
EST:     CCATCATTCTGCACTCTGCACTGATTACCAACCTCTATTTCATATCCCAG                         CTTCTCTACAGGAAGTACAGTGGAAACTTCCTTGTTAACCTTCTTGGGATG
genomic: CCATCATTCTGCACTCTGCACTGATTACCAACCTCTATTTCATATCCCAGgtacgcacct ... gctatcacagCTTCTCTACAGGAAGTACAGTGGAAACTTCCTTGTTAACCTTCTTGGGATG
EST: gi|32838942|gb|CD978623.1|CD978623
EST:     CCATCATTCTGCACTCTGCACTGATTACCAACCTCTATTTCATATCCCAG                         CTTCTCTACAGGAAGTA
genomic: CCATCATTCTGCACTCTGCACTGATTACCAACCTCTATTTCATATCCCAGgtacgcacct ... gctatcacagCTTCTCTACAGGAAGTA
EST: gi|71425883|gb|DR806950.1|DR806950
EST:     CCATCATTCTGCACTCTGCACTGATTACCAACCTCTATTTCATATCCCAG                         CTTCTCTACAGGAAGTACAGTGGAAACTTCCTTGTTAACCTTCTTGGGATG
genomic: CCATCATTCTGCACTCTGCACTGATTACCAACCTCTATTTCATATCCCAGgtacgcacct ... gctatcacagCTTCTCTACAGGAAGTACAGTGGAAACTTCCTTGTTAACCTTCTTGGGATG
EST: gi|32858247|gb|CD997928.1|CD997928
EST:     CCATCATTCTGCACTCTGCACTGATTACCAACCTCTATTTCATATCCCAG                         CTTCTCTACAGGAAGTACAGTGGAAACTTCCTTGTTAACCTTCTTGGGATG
genomic: CCATCATTCTGCACTCTGCACTGATTACCAACCTCTATTTCATATCCCAGgtacgcacct ... gctatcacagCTTCTCTACAGGAAGTACAGTGGAAACTTCCTTGTTAACCTTCTTGGGATG
EST: gi|32934776|gb|CF039588.1|CF039588
EST:     CCATCATTCTGCACTCTGCACTGATTACCAACCTCTATTTCATATCCCAG                         CTTCTCTACAGGAAGTAC
genomic: CCATCATTCTGCACTCTGCACTGATTACCAACCTCTATTTCATATCCCAGgtacgcacct ... gctatcacagCTTCTCTACAGGAAGTAC
EST: gi|211338836|gb|FL045913.1|FL045913
EST:     CCATCATTCTGCACTCTGCACTGATTACCAACCTCTATTTCATATCCCAG                         CTTCTCTACAGGAAGTACAGTGGAAACTTCCTTGTTAACCTTCTTGGGATG
genomic: CCATCATTCTGCACTCTGCACTGATTACCAACCTCTATTTCATATCCCAGgtacgcacct ... gctatcacagCTTCTCTACAGGAAGTACAGTGGAAACTTCCTTGTTAACCTTCTTGGGATG
EST: gi|31354346|gb|CD438703.1|CD438703
EST:     CCATCATTCTGCACTCTGCACTGATTACCAACCTCTATTTCATATCCCAG                         CTTCTCTACAGGAAGTACAGTGGAAACTTCCTTGTTAACCTTCTTGGGATG
genomic: CCATCATTCTGCACTCTGCACTGATTACCAACCTCTATTTCATATCCCAGgtacgcacct ... gctatcacagCTTCTCTACAGGAAGTACAGTGGAAACTTCCTTGTTAACCTTCTTGGGATG

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: 1015

TGGCCAGCAAGGCTCATATCCAATTAAGCTATTCTACACTTCAAACATGCCCATCATTCTGCACTCTGCACTGATTACCAACCTCTATTTCATATCCCAGgtacgcacct ... gctatcacagCTTCTCTACAGGAAGTACAGTGGAAACTTCCTTGTTAACCTTCTTGGGATGTGGAAGGAGTCTGAATACTCTGGCCATTCTGTTCCTGTTGGTGGTCTTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 941

TGGCCAGCAAGGCTCATATCCAATTAAGCTATTCTACACTTCAAACATGCCCATCATTCTGCACTCTGCACTGATTACCAACCTCTATTTCATATCCCAGgtacgcacct ... gctatcacagCTTCTCTACAGGAAGTACAGTGGAAACTTCCTTGTTAACCTTCTTGGGATGTGGAAGGAGTCTGAATACTCTGGCCATTCTGTTCCTGTTGGTGGTCTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1188

TGGCCAGCAAGGCTCATATCCAATTAAGCTATTCTACACTTCAAACATGCCCATCATTCTGCACTCTGCACTGATTACCAACCTCTATTTCATATCCCAGgtacgcacct ... gctatcacagCTTCTCTACAGGAAGTACAGTGGAAACTTCCTTGTTAACCTTCTTGGGATGTGGAAGGAGTCTGAATACTCTGGCCATTCTGTTCCTGTTGGTGGTCTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1256

TGGCCAGCAAGGCTCATATCCAATTAAGCTATTCTACACTTCAAACATGCCCATCATTCTGCACTCTGCACTGATTACCAACCTCTATTTCATATCCCAGgtacgcacct ... gctatcacagCTTCTCTACAGGAAGTACAGTGGAAACTTCCTTGTTAACCTTCTTGGGATGTGGAAGGAGTCTGAATACTCTGGCCATTCTGTTCCTGTTGGTGGTCTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtcatgtcttctgtgtgtatgtgtaaatgctgatgtattttattgctatcacagCTTCTCTACAGGAAGTACAGTGGAAACTTCCTTGTTAACCTTCTTGGGATGTGGAAGGAGTCTGAATACTCTGGCCATTCTGTTCCTGTTGGTGGTCTTG
                            tgctgat  putative branch site (score: 1256)
                               tgatgtattttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgcacctcatttccaatgctgtagtaagtcatgtcttctgtgtgtatgtgtaaatgctgatgtattttattgctatcacagCTTCTCTACAGGAAGTACAGTGGAAACTTCCTTGTTAACCTTCTTGGGATGTGGAAGGAGTCTGAATACTCTGGCCATTCTGTTCCTGTTGGTGGTCTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG