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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtacttttgaactcaatgacctgttaccttgtcaatttcaaccacattaaaaatctagctcctaaccactcctggatgaatgcaacctgcagGTCTGGTTCAGTCTGTTTGGATGTCATCAACCAGACATGGAGCCCAATGTTTG

Basic information

species Zea mays
transcript GRMZM2G150867_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G150867_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os10g31000.1 (Oryza sativa), 3'ss of exon 3
gtgagtacttttgaactcaatgacctgttaccttgtcaatttcaaccacattaaaaatctagctcctaaccactcctggatgaatgcaacctgcagGTCTGGTTCAGTCTGTTTGGATGTCATCAACCAGACATGGAGCCCAATGTTTG
||||| |  |||||  || ||  ||| || |       |||  | |     |||  |  |    |  | |  ||  ||   || |  ||  || ||||||||||| || |||||||||||||| |||||||| ||||||||||||||||
gtgagga--tttgatgtccataccctttt-ctggaatgattgaagcttgtgtaatcaattgttgctgacctgcttttgttggacttgaaaatgtagGTCTGGTTCTGTGTGTTTGGATGTCATTAACCAGACGTGGAGCCCAATGTTTG

upper sequence: GRMZM2G150867_T02 (Zea mays), 3'ss of exon 3
lower sequence: Vv02s0025g00070.t01 (Vitis vinifera), 3'ss of exon 3
----------------------gtgagtacttttgaactcaatgacctg---ttaccttgtcaatttcaaccacattaaaaatctagct--cctaaccac-----tcctggatgaatgcaacctgcagGTCTGGTTCAGTCTGTTTGGATGTCATCAACCAGACATGGAGCCCAATGTTTG
                         |||||||  |    || ||| |||   ||  ||| |  ||  ||| || |   || |  | | |  |  ||  |      || ||   |  |   |  | ||||||||||||||| ||||| ||||||||||| ||||| ||||||||||||||||
gtgagttagtggatgtttaaaacctagtacttcagcttgca-tgagctgcatttttcttatatatgacaaacataaggaagaattggttttctcaaatatgacaatcttgtgggtctttgagtttcagGTCTGGTTCAGTTTGTTTAGATGTCATCAATCAGACTTGGAGCCCAATGTTTG
















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|6056913|gb|AW091318.1|AW091318
EST:     CCATCGATTGGTTTCATCAATAAGATATATCACCCAAATGTCGATGAAAT                         GTCTGGTTCAGTCTGTTTGGATGTCATCAACCAGACATGGAGCCCAATGTT
genomic: CCATCGATTGGTTTCATCAATAAGATATATCACCCAAATGTCGATGAAATgtgagtactt ... caacctgcagGTCTGGTTCAGTCTGTTTGGATGTCATCAACCAGACATGGAGCCCAATGTT
EST: gi|211541025|gb|FL000900.1|FL000900
EST:     CCATCGATTGGTTTCATCAATAAGATATATCACCCAAATGTCGATGAAAT                         GTCTGGTTCAGTCTGTTTGGATGTCATCAACCAGACATGGAGCCCAATGTT
genomic: CCATCGATTGGTTTCATCAATAAGATATATCACCCAAATGTCGATGAAATgtgagtactt ... caacctgcagGTCTGGTTCAGTCTGTTTGGATGTCATCAACCAGACATGGAGCCCAATGTT
EST: gi|26559982|gb|CA832217.1|CA832217
EST:     CCATCGATTGGTTTCATCAATAAGATATATCACCCAAATGTCGATGAAAT                         GTCTGGTTCAGTCTGTTTGGATGTCATCAACCAGACATGGAGCCCAATGTT
genomic: CCATCGATTGGTTTCATCAATAAGATATATCACCCAAATGTCGATGAAATgtgagtactt ... caacctgcagGTCTGGTTCAGTCTGTTTGGATGTCATCAACCAGACATGGAGCCCAATGTT
EST: gi|15499388|gb|BI595901.1|BI595901
EST:     CCATCGATTGGTTTCATCAATAAGATATATCACCCAAATGTCGATGAAAT                         GTCTGGTTCAGTCTGTTTGGATGTCATCAACCAGACATGGAGCCCAATGTT
genomic: CCATCGATTGGTTTCATCAATAAGATATATCACCCAAATGTCGATGAAATgtgagtactt ... caacctgcagGTCTGGTTCAGTCTGTTTGGATGTCATCAACCAGACATGGAGCCCAATGTT
EST: gi|211541022|gb|FL000897.1|FL000897
EST:     CCATCGATTGGTTTCATCAATAAGATATATCACCCAAATGTCGATGAAAT                         GTCTGGTTCAGTCTGTTTGGATGTCATCAACCAGACATGGAGCCCAATGTT
genomic: CCATCGATTGGTTTCATCAATAAGATATATCACCCAAATGTCGATGAAATgtgagtactt ... caacctgcagGTCTGGTTCAGTCTGTTTGGATGTCATCAACCAGACATGGAGCCCAATGTT
EST: gi|87157692|gb|DY402481.1|DY402481
EST:     CCATCGATTGGTTTCATCAATAAGATATATCACCCAAATGTCGATGAAAT                         GTCTGGTTCAGTCTGTTTGGATGTCATCAACCAGACATGGAGCCCAATGTT
genomic: CCATCGATTGGTTTCATCAATAAGATATATCACCCAAATGTCGATGAAATgtgagtactt ... caacctgcagGTCTGGTTCAGTCTGTTTGGATGTCATCAACCAGACATGGAGCCCAATGTT
EST: gi|33103947|gb|CF063907.1|CF063907
EST:     CCATCGATTGGTTTCATCAATAAGATATATCACCCAAATGTCGATGAAAT                         GTCTGGTTCAGTCTGTTTGGATGTCATCAACCAGACATGGAGCCCAATGTT
genomic: CCATCGATTGGTTTCATCAATAAGATATATCACCCAAATGTCGATGAAATgtgagtactt ... caacctgcagGTCTGGTTCAGTCTGTTTGGATGTCATCAACCAGACATGGAGCCCAATGTT
EST: gi|12971358|gb|BG267442.1|BG267442
EST:     CCATCGATTGGTTTCATCAATAAGATATATCACCCAAATGTCGATGAAAT                         GTCTGGTTCAGTCTGTTTGGATGTCATCAACCAGACATGGAGCCCAATGTT
genomic: CCATCGATTGGTTTCATCAATAAGATATATCACCCAAATGTCGATGAAATgtgagtactt ... caacctgcagGTCTGGTTCAGTCTGTTTGGATGTCATCAACCAGACATGGAGCCCAATGTT
EST: gi|28984207|gb|BQ538996.2|BQ538996
EST:     CCATCGATTGGTTTCATCAATAAGATATATCACCCAAATGTCGATGAAAT                         GTCTGGTTCAGTCTGTTTGGATGTCATCAACCAGACATGGAGCCCAATGTT
genomic: CCATCGATTGGTTTCATCAATAAGATATATCACCCAAATGTCGATGAAATgtgagtactt ... caacctgcagGTCTGGTTCAGTCTGTTTGGATGTCATCAACCAGACATGGAGCCCAATGTT
EST: gi|23199807|gb|BU582372.1|BU582372
EST:     CCATCGATTGGTTTCATCAATAAGATATATCACCCAAATGTCGATGAAAT                         GTCTGGTTCAGTCTGTTTGGATGTCATCAACCAGACATGGAGCCCAATGTT
genomic: CCATCGATTGGTTTCATCAATAAGATATATCACCCAAATGTCGATGAAATgtgagtactt ... caacctgcagGTCTGGTTCAGTCTGTTTGGATGTCATCAACCAGACATGGAGCCCAATGTT
EST: gi|211541028|gb|FL000903.1|FL000903
EST:     CCATCGATTGGTTTCATCAATAAGATATATCACCCAAATGTCGATGAAAT                         GTCTGGTTCAGTCTGTTTGGATGTCATCAACCAGACATGGAGCC-AATGTT
genomic: CCATCGATTGGTTTCATCAATAAGATATATCACCCAAATGTCGATGAAATgtgagtactt ... caacctgcagGTCTGGTTCAGTCTGTTTGGATGTCATCAACCAGACATGGAGCCCAATGTT
EST: gi|211541020|gb|FL000895.1|FL000895
EST:     CCATCGATTGGTTTCATCAATAAGATATATCACCCAAATGTCGATGAAAT                         GTCTGGTTCAGTCTGTTTGGATGTCATCAACCAGACATGGAGCCCAATGTT
genomic: CCATCGATTGGTTTCATCAATAAGATATATCACCCAAATGTCGATGAAATgtgagtactt ... caacctgcagGTCTGGTTCAGTCTGTTTGGATGTCATCAACCAGACATGGAGCCCAATGTT
EST: gi|15427006|gb|BI542828.1|BI542828
EST:     CCATCGATTGGTTTCATCAATAAGATATATCACCCAAATGTCGATGAAAT                         GTCTGGTTCAGTCTGTTTGGATGTCATCAACCAGACATGGAGCCCAATGTT
genomic: CCATCGATTGGTTTCATCAATAAGATATATCACCCAAATGTCGATGAAATgtgagtactt ... caacctgcagGTCTGGTTCAGTCTGTTTGGATGTCATCAACCAGACATGGAGCCCAATGTT
EST: gi|5439433|gb|AI820354.1|AI820354
EST:     CCATCGATTGGTTTCATCAATAAGATATATCACCCAAATGTCGATGAAAT                         GTCTGGTTCAGTCTGTTTGGATGTCATCAACCAGACATGGAGCCCAATGTT
genomic: CCATCGATTGGTTTCATCAATAAGATATATCACCCAAATGTCGATGAAATgtgagtactt ... caacctgcagGTCTGGTTCAGTCTGTTTGGATGTCATCAACCAGACATGGAGCCCAATGTT
EST: gi|211541021|gb|FL000896.1|FL000896
EST:     CCATCGATTGGTTTCATCAATAAGATATATCACCCAAATGTCGATGAAAT                         GTCTGGTTCAGTCTGTTTGGATGTCATCAACCAGACATGGAGCCCAATGTT
genomic: CCATCGATTGGTTTCATCAATAAGATATATCACCCAAATGTCGATGAAATgtgagtactt ... caacctgcagGTCTGGTTCAGTCTGTTTGGATGTCATCAACCAGACATGGAGCCCAATGTT
EST: gi|211541018|gb|FL000893.1|FL000893
EST:     CCATCGATTGGTTTCATCAATAAGATATATCACCCAAATGTCGATGAAAT                         GTCTGGTTCAGTCTGTTTGGATGTCATCAACCAGACATGGAGCCCAATGTT
genomic: CCATCGATTGGTTTCATCAATAAGATATATCACCCAAATGTCGATGAAATgtgagtactt ... caacctgcagGTCTGGTTCAGTCTGTTTGGATGTCATCAACCAGACATGGAGCCCAATGTT
EST: gi|84980137|gb|DW530486.1|DW530486
EST:     CCATCGATTGGTTTCATCAATAAGATATATCACCCAAATGTCGATGAAAT                         GTCTGGTTCAGTCTGTTTGGATGTCATCAACCAGACATGGAGCCCAATGTT
genomic: CCATCGATTGGTTTCATCAATAAGATATATCACCCAAATGTCGATGAAATgtgagtactt ... caacctgcagGTCTGGTTCAGTCTGTTTGGATGTCATCAACCAGACATGGAGCCCAATGTT
EST: gi|37394410|gb|CF634479.1|CF634479
EST:     CCATCGATTGGTTTCATCAATAAGATATATCACCCAAATGTCGATGAAAT                         GTCTGGTTCAGTCTGTTTGGATGTCATCAACCAGACATGGAGCCCAATGTT
genomic: CCATCGATTGGTTTCATCAATAAGATATATCACCCAAATGTCGATGAAATgtgagtactt ... caacctgcagGTCTGGTTCAGTCTGTTTGGATGTCATCAACCAGACATGGAGCCCAATGTT
EST: gi|5455873|gb|AI833563.1|AI833563
EST:     CCATCGATTGGTTTCATCAATAAGATATATCACCCAAATGTCGATGAAAT                         GTCTGGTTCAGTCTGTTTGGATGTCATCAACCAGACATGGAGCCCAATGTT
genomic: CCATCGATTGGTTTCATCAATAAGATATATCACCCAAATGTCGATGAAATgtgagtactt ... caacctgcagGTCTGGTTCAGTCTGTTTGGATGTCATCAACCAGACATGGAGCCCAATGTT
EST: gi|5525634|gb|AI861527.1|AI861527
EST:     CCNTCGATTGGTTTCATCAATAAGATATATCACCCAAATGTCGATGAAAT                         GTCTGGTTCAGTCTGTTTGGATGTCATCAACCAGACATGGAGCCCAATGTT
genomic: CCATCGATTGGTTTCATCAATAAGATATATCACCCAAATGTCGATGAAATgtgagtactt ... caacctgcagGTCTGGTTCAGTCTGTTTGGATGTCATCAACCAGACATGGAGCCCAATGTT
EST: gi|32911041|gb|CF015853.1|CF015853
EST:     CCATCGATTGGTTTCATCAATAAGATATATCACCCAAATGTCGATGAAAT                         GTCTGGTTCAGTCTGTTTGGATGTCATCAACCAGACATGGAGCCCAATGTT
genomic: CCATCGATTGGTTTCATCAATAAGATATATCACCCAAATGTCGATGAAATgtgagtactt ... caacctgcagGTCTGGTTCAGTCTGTTTGGATGTCATCAACCAGACATGGAGCCCAATGTT
EST: gi|211541027|gb|FL000902.1|FL000902
EST:     CCATCGATTGGTTTCATCAATAAGATATATCACCCAAATGTCGATGAAAT                         GTCTGGTTCAGTCTGTTTGGATGTCATCAACCAGACATGGAGCCCCATGTT
genomic: CCATCGATTGGTTTCATCAATAAGATATATCACCCAAATGTCGATGAAATgtgagtactt ... caacctgcagGTCTGGTTCAGTCTGTTTGGATGTCATCAACCAGACATGGAGCCCAATGTT
EST: gi|211096443|gb|FL454804.1|FL454804
EST:     CCATCGATT-GTTTCATCAATAAGATATATCACCCAAATGTCGATGAAAT                         GTCTGGTTCAGTCTGTTTGGATGTCATCAACCAGACATGGAGCCCAATGTT
genomic: CCATCGATTGGTTTCATCAATAAGATATATCACCCAAATGTCGATGAAATgtgagtactt ... caacctgcagGTCTGGTTCAGTCTGTTTGGATGTCATCAACCAGACATGGAGCCCAATGTT

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), 49 (downstream exon)
Score: 179

GTATATGGAGGGTTAGAGTAGAACTGCCAGATGCGTATCCTTACAAATCCCCATCGATTGGTTTCATCAATAAGATATATCACCCAAATGTCGATGAAATgtgagtactt ... caacctgcagGTCTGGTTCAGTCTGTTTGGATGTCATCAACCAGACATGGAGCCCAATGTTTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 317

GTATATGGAGGGTTAGAGTAGAACTGCCAGATGCGTATCCTTACAAATCCCCATCGATTGGTTTCATCAATAAGATATATCACCCAAATGTCGATGAAATgtgagtactt ... caacctgcagGTCTGGTTCAGTCTGTTTGGATGTCATCAACCAGACATGGAGCCCAATGTTTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 233

GTATATGGAGGGTTAGAGTAGAACTGCCAGATGCGTATCCTTACAAATCCCCATCGATTGGTTTCATCAATAAGATATATCACCCAAATGTCGATGAAATgtgagtactt ... caacctgcagGTCTGGTTCAGTCTGTTTGGATGTCATCAACCAGACATGGAGCCCAATGTTTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 213

GTATATGGAGGGTTAGAGTAGAACTGCCAGATGCGTATCCTTACAAATCCCCATCGATTGGTTTCATCAATAAGATATATCACCCAAATGTCGATGAAATgtgagtactt ... caacctgcagGTCTGGTTCAGTCTGTTTGGATGTCATCAACCAGACATGGAGCCCAATGTTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaaccacattaaaaatctagctcctaaccactcctggatgaatgcaacctgcagGTCTGGTTCAGTCTGTTTGGATGTCATCAACCAGACATGGAGCCCAATGTTTG
                      tcctaac  putative branch site (score: 213)
      acattaaaaatcta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtacttttgaactcaatgacctgttaccttgtcaatttcaaccacattaaaaatctagctcctaaccactcctggatgaatgcaacctgcagGTCTGGTTCAGTCTGTTTGGATGTCATCAACCAGACATGGAGCCCAATGTTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA