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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACCTTATCTCAATTGACATCTGGAAAACAACCTGTTGGTACAATGGCTTACATGGGCAATGTACAATATCTGATGCAATGCAAATGTGCTGTTAACACAGgtacttatttaggctggatcattatattttctagttctcagttatatttgatatttgttccaggcttcttgaggataatgtctgtattgactatggtataattcatgtttggtgactcaacag

Basic information

species Zea mays
transcript GRMZM5G864319_T01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G864319_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os06g01390.1 (Oryza sativa), 5'ss of exon 10
ACCTTATCTCAATTGACATCTGGAAAACAACCTGTTGGTACAATGGCTTACATGGGCAATGTACAATATCTGATGCAATGCAAATGTGCTGTTAACACAGgtacttattta--------ggctggatc--attata--------ttttctagttctcagt-tatatttgatatttgttccaggcttcttgagga-----taatgtctgtattgactatggtataattcatgtttg-gtgact--caacag
||  |||| || ||  | ||||||||||| ||||||||||||| |||||||||||||||  |||| ||  |||||||||||||||||| ||| || |||||||  || ||         ||| || ||   || ||        | | | |||  ||| | ||  ||   ||| | |       ||  || | |     | ||||    ||  |        | |||||| |||   ||| |  | ||||
ACTGTATCCCAGTTAGCTTCTGGAAAACAGCCTGTTGGTACAACGGCTTACATGGGCAACATACAGTACTTGATGCAATGCAAATGTGGTGTAAATACAGgtatatagttgtatcttctggcaggctcctgttttagacagctgtatgccagtcatcactgtacgttatgtatatatatgcccattgctgggaagccattgatgttgagatgaatgccatagtgattcatttttccatgattatcgacag
















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|33104324|gb|CF064284.1|CF064284
EST:     CATGGGCAATGTACAATATCTGATGCAATGCAAATGTGCTGTTAACACAG                         CCGAAGATTGGCTTAACCCTGTTGCCATACAAGAGGCGTTTGAAGCCCGGG
genomic: CATGGGCAATGTACAATATCTGATGCAATGCAAATGTGCTGTTAACACAGgtacttattt ... gactcaacagCTGAAGATTGGCTTAACCCTGTTGCCATACAAGAGGCGTTTGAAGCCAGGG
EST: gi|32835294|gb|CD974972.1|CD974972
EST:     GTACAATATCTGATGCAATGCAAATGTGCTGTTAACACAG                         CTGAAGATTGGCTTAACCCTGTTGCCATACAAGAGGCGTTTGAAGCCAGGG
genomic: GTACAATATCTGATGCAATGCAAATGTGCTGTTAACACAGgtacttattt ... gactcaacagCTGAAGATTGGCTTAACCCTGTTGCCATACAAGAGGCGTTTGAAGCCAGGG
EST: gi|32834719|gb|CD974397.1|CD974397
EST:     GTACAATATCTGATGCAATGCAAATGTGCTGTTAACACAG                         CTGAAGATTGGCTTAACCCTGTTGCCATACAAGAGGCGTTTGAAGCCAGGG
genomic: GTACAATATCTGATGCAATGCAAATGTGCTGTTAACACAGgtacttattt ... gactcaacagCTGAAGATTGGCTTAACCCTGTTGCCATACAAGAGGCGTTTGAAGCCAGGG
EST: gi|113703173|gb|EE680677.1|EE680677
EST:     ATGCAAATGTGCTGTTAACACAG                         CTGAAGATTGGCTTAACCCTGTTGCCATACAAGAGGCGTTTGAAGCCAGGG
genomic: ATGCAAATGTGCTGTTAACACAGgtacttattt ... gactcaacagCTGAAGATTGGCTTAACCCTGTTGCCATACAAGAGGCGTTTGAAGCCAGGG
EST: gi|19436236|gb|BM952646.1|BM952646
EST:     CATGGGCAATGTACAATATCTGATGCAATGCAAATGTGCTGTTAACACAG                         CTGAAGATTGGCTTAACCCTGTTGCCATACAAGAGGCGTTTGAAGCCAGGG
genomic: CATGGGCAATGTACAATATCTGATGCAATGCAAATGTGCTGTTAACACAGgtacttattt ... gactcaacagCTGAAGATTGGCTTAACCCTGTTGCCATACAAGAGGCGTTTGAAGCCAGGG
EST: gi|213179269|gb|FM196444.1|FM196444
EST:     CATGGGCAATGTACAATATCTGATGCAATGCAAATGTGCTGTTAACACAG                         CTGAAGATTGGCTTAACCCTGTTGCCATACAAGAGGCGTTTGAAGCCAGGG
genomic: CATGGGCAATGTACAATATCTGATGCAATGCAAATGTGCTGTTAACACAGgtacttattt ... gactcaacagCTGAAGATTGGCTTAACCCTGTTGCCATACAAGAGGCGTTTGAAGCCAGGG
EST: gi|9732140|gb|BE510892.1|BE510892
EST:     ATGGGCAATGTTCTATTATCTGATGCAATGCAAATGTGCTGTTAACACAG                         CCGAAGATTGGCTTAACCCTGTTGCCATACAAGAGGCGTTTGAAGCCCGGG
genomic: ATGGGCAATGTAC-AATATCTGATGCAATGCAAATGTGCTGTTAACACAGgtacttattt ... gactcaacagCTGAAGATTGGCTTAACCCTGTTGCCATACAAGAGGCGTTTGAAGCCAGGG
EST: gi|22490101|gb|BU050024.1|BU050024
EST:     CATGGGCAATGTACAATATCTGATGCAATGCAAATGTGCTGTTAACACAG                         CTGAAGATTGGCTTAACCCTGTTGCCATACAAGAGGCGTTTGAAGCCAGGG
genomic: CATGGGCAATGTACAATATCTGATGCAATGCAAATGTGCTGTTAACACAGgtacttattt ... gactcaacagCTGAAGATTGGCTTAACCCTGTTGCCATACAAGAGGCGTTTGAAGCCAGGG
EST: gi|19351144|gb|BM895676.1|BM895676
EST:     CATGGGCAATGTACAATATCTGATGCAATGCAAATGTGCTGTTAACACAG                         CTGAAGATTGGCTTAACCCTGTTGCCATACAAGAGGCGTTTGAAGCCAGGG
genomic: CATGGGCAATGTACAATATCTGATGCAATGCAAATGTGCTGTTAACACAGgtacttattt ... gactcaacagCTGAAGATTGGCTTAACCCTGTTGCCATACAAGAGGCGTTTGAAGCCAGGG
EST: gi|33101745|gb|CF061705.1|CF061705
EST:     CATGGGCAATGTACAATATCTGATGCAATGCAAATGTGCTGTTAACACAG                         CCGAAGATTGGCTTAACCCTGTTGCCATACAAGAGGCGTTTGAAGCCCGGG
genomic: CATGGGCAATGTACAATATCTGATGCAATGCAAATGTGCTGTTAACACAGgtacttattt ... gactcaacagCTGAAGATTGGCTTAACCCTGTTGCCATACAAGAGGCGTTTGAAGCCAGGG
EST: gi|18655285|gb|BM500090.1|BM500090
EST:     CATGGGCAATGTACAATATCTGATGCAATGCAAATGTGCTGTTAACACAG                         CTGAAGATTGGCTTAACCCTGTTGCCATACAAGAGGCGTTTGAAGCCAGGG
genomic: CATGGGCAATGTACAATATCTGATGCAATGCAAATGTGCTGTTAACACAGgtacttattt ... gactcaacagCTGAAGATTGGCTTAACCCTGTTGCCATACAAGAGGCGTTTGAAGCCAGGG
EST: gi|60358249|gb|DN225222.1|DN225222
EST:     CATGGGCAATGTACAATATCTGATGCAATGCAAATGTGCTGTTAACACAG                         CCGAAGATTGGCTTAACCCTGTTGCCATACAAGAGGCGTTTGAAGCCCGGG
genomic: CATGGGCAATGTACAATATCTGATGCAATGCAAATGTGCTGTTAACACAGgtacttattt ... gactcaacagCTGAAGATTGGCTTAACCCTGTTGCCATACAAGAGGCGTTTGAAGCCAGGG
EST: gi|14204220|gb|BG837897.1|BG837897
EST:     CATGGGCAATGTACAATATCTGATGCAATGCAAATGTGCTGTTAACACAG                         CTGAAGATTGGCTTAACCCTGTTGCCATACAAGAGGCGTTTGAAGCCAGGG
genomic: CATGGGCAATGTACAATATCTGATGCAATGCAAATGTGCTGTTAACACAGgtacttattt ... gactcaacagCTGAAGATTGGCTTAACCCTGTTGCCATACAAGAGGCGTTTGAAGCCAGGG
EST: gi|87153521|gb|DY398310.1|DY398310
EST:     CATGGGCAATGTACAATATCTGATGCAATGCAAATGTGCTGTTAACACAG                         CTGAAGATTGGCTTAACCCTGTTGCCATACAAGAGGCGTTTGAAGCCAGGG
genomic: CATGGGCAATGTACAATATCTGATGCAATGCAAATGTGCTGTTAACACAGgtacttattt ... gactcaacagCTGAAGATTGGCTTAACCCTGTTGCCATACAAGAGGCGTTTGAAGCCAGGG

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: 238

ACCTTATCTCAATTGACATCTGGAAAACAACCTGTTGGTACAATGGCTTACATGGGCAATGTACAATATCTGATGCAATGCAAATGTGCTGTTAACACAGgtacttattt ... gactcaacagCTGAAGATTGGCTTAACCCTGTTGCCATACAAGAGGCGTTTGAAGCCAGGGCTCTCAGGATGGCAGTAAACTGTGCCCAGAACATAGGCCAAGCAGCAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 563

ACCTTATCTCAATTGACATCTGGAAAACAACCTGTTGGTACAATGGCTTACATGGGCAATGTACAATATCTGATGCAATGCAAATGTGCTGTTAACACAGgtacttattt ... gactcaacagCTGAAGATTGGCTTAACCCTGTTGCCATACAAGAGGCGTTTGAAGCCAGGGCTCTCAGGATGGCAGTAAACTGTGCCCAGAACATAGGCCAAGCAGCAAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 784

ACCTTATCTCAATTGACATCTGGAAAACAACCTGTTGGTACAATGGCTTACATGGGCAATGTACAATATCTGATGCAATGCAAATGTGCTGTTAACACAGgtacttattt ... gactcaacagCTGAAGATTGGCTTAACCCTGTTGCCATACAAGAGGCGTTTGAAGCCAGGGCTCTCAGGATGGCAGTAAACTGTGCCCAGAACATAGGCCAAGCAGCAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 987

ACCTTATCTCAATTGACATCTGGAAAACAACCTGTTGGTACAATGGCTTACATGGGCAATGTACAATATCTGATGCAATGCAAATGTGCTGTTAACACAGgtacttattt ... gactcaacagCTGAAGATTGGCTTAACCCTGTTGCCATACAAGAGGCGTTTGAAGCCAGGGCTCTCAGGATGGCAGTAAACTGTGCCCAGAACATAGGCCAAGCAGCAAA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACCTTATCTCAATTGACATCTGGAAAACAACCTGTTGGTACAATGGCTTACATGGGCAATGTACAATATCTGATGCAATGCAAATGTGCTGTTAACACAGgtacttatttaggctggatcattatattttctagttctcagttatatttgatatttgttccaggcttcttgaggataatgtctgtattgactatggtataattcatgtttggtgactcaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT