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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTTGTTTCATCAGTGGATAAAAAGCTGGAGGTTAAACCACGTTTTTTGGAAATTTTTCAAGAAGACAACTACCCTACAGAGTTCCCTTACAAGTCCAAGgtaagaattcattcttgtcatttgaagcatgaatcgtagttacactcactaatttctgcaacactattttttatgaaatgttggacag

Basic information

species Zea mays
transcript GRMZM2G470556_T01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G470556_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os02g04490.1 (Oryza sativa), 5'ss of exon 9
AGTTGTTTCATCAGTGGATAAAAAGCTGGAGGTTAAACCACGTTTTTTGGAAATTTTTCAAGAAGACAACTACCCTACAGAGTTCCCTTACAAGTCCAAGgtaagaattcattcttg---tcatttgaagcatgaatcgtagttacactcactaatt-tctgcaacactattttttatgaaatgttggacag
|||||||||||||||||| || |||||||| || |||||||||||||||||||||||||||||||| |||||||| ||||||||||| ||||||||||||||||||| | | ||  |   || ||  ||  |  |    |  || ||  ||  |||  |  |  | ||| |||||||| ||||||| | |||
AGTTGTTTCATCAGTGGACAAGAAGCTGGAAGTAAAACCACGTTTTTTGGAAATTTTTCAAGAAGATAACTACCCGACAGAGTTCCCATACAAGTCCAAGgtaagaaattagtccagtattctttcaaaagaacaccaatcatttcaagcataaatcatacgtgaaactgttttttatcaaatgtttggcag

upper sequence: GRMZM2G470556_T01 (Zea mays), 5'ss of exon 8
lower sequence: PP1S193_70V6.1 (Physcomitrella patens), 5'ss of exon 10
AGTTGTTTCATCAGTGGATAAAAAGCTGGAGGTTAAACCACGTTTTTTGGAAATTTTTCAAGAAGACAACTACCCTACAGAGTTCCCTTACAAGTCCAAGgtaagaattcattcttgtcatttgaagcatgaatcgtagttacactcactaatttctgcaacactattttttatgaaatgttggacag-------------------------------------------------------------
|||||| || || ||||| || |||||||| || || | ||| |||||||||||||||||||||||  |||| || || || |  || |||||||| ||||||     |  | |||||  |||   |     | |  |||| | |   ||  | | | ||| |||  | || | ||  | || |                                                                 
AGTTGTGTCCTCTGTGGACAAGAAGCTGGAAGTCAAGCAACGGTTTTTGGAAATTTTTCAAGAAGAAGACTATCCAACTGAATATCCATACAAGTCGAAGgtata---ttttgcttgtggtttagtgtggccaacaaagtttc-caagcttgtcttt-caaaactcatgttcacgatgtttttgctttgtggtttcaatgttaatataagcgtatttatagggacttgtttgctatttttgttattcag
















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|211057050|gb|FL391369.1|FL391369
EST:     AATTTTTCAAGAAGACAACTACCCTACAGAGTTCCCTTACAAGGTCCAAG                         GCTGTTCTCTTGTTCCAGAGAATAGAAGGTGTGGAAGTATGTCTATTTGG
genomic: AATTTTTCAAGAAGACAACTACCCTACAGAGTTCCCTTACAA-GTCCAAGgtaagaattc ... tgttggacagGCTGTTCTCTTGTTCCAGAGAATAGAAGGTGTGGAAGTATGTCTATTTGG
EST: gi|211363258|gb|FL387051.1|FL387051
EST:     AAATTTTTCAAGAAGACAACTACCCTACAGAGTTCCCTTACAAGTCCAAG                         GCTGTTCTCTTGTTCCAGAGAATAGAAGGTGTGGAAGTATGTCTATTTGGC
genomic: AAATTTTTCAAGAAGACAACTACCCTACAGAGTTCCCTTACAAGTCCAAGgtaagaattc ... tgttggacagGCTGTTCTCTTGTTCCAGAGAATAGAAGGTGTGGAAGTATGTCTATTTGGC
EST: gi|211299426|gb|FL430297.1|FL430297
EST:     AAATTTTTCAAGAAGACAACTACCCTACAGAGTTCCCTTACAAGTCCAAG                         GCTGTTCTCTTGTTCCAGAGAATAGAAGGTGTGGAAGTATGTCTATTTGGC
genomic: AAATTTTTCAAGAAGACAACTACCCTACAGAGTTCCCTTACAAGTCCAAGgtaagaattc ... tgttggacagGCTGTTCTCTTGTTCCAGAGAATAGAAGGTGTGGAAGTATGTCTATTTGGC
EST: gi|211235994|gb|FL378061.1|FL378061
EST:     AAATTTTTCAAGAAGACAACTACCCTACAGAGTTCCCTTACAAGTCCAAG                         GCTGTTCTCTTGTTCCAGAGAATAGAAAGGTGTGGAAGTATGTCTATTTGG
genomic: AAATTTTTCAAGAAGACAACTACCCTACAGAGTTCCCTTACAAGTCCAAGgtaagaattc ... tgttggacagGCTGTTCTCTTGTTCCAGAGAATAG-AAGGTGTGGAAGTATGTCTATTTGG
EST: gi|211299429|gb|FL430300.1|FL430300
EST:     AAATTTTTCAAGAAGACAACTACCCTACAGAGTTCCCTTACAAGTCCAAG                         GCTGGTCTCTTGTTCC
genomic: AAATTTTTCAAGAAGACAACTACCCTACAGAGTTCCCTTACAAGTCCAAGgtaagaattc ... tgttggacagGCTGTTCTCTTGTTCC
EST: gi|211022186|gb|FL381963.1|FL381963
EST:     AAATTTTTCAAGAAGACAACTACCCTACAGAGTTCCCTTACAAGTCCAAG                         GCTGTTCTCTTGTTCCAGAGAATANAAGGTGTGGAAGTATGTCTATTTGGC
genomic: AAATTTTTCAAGAAGACAACTACCCTACAGAGTTCCCTTACAAGTCCAAGgtaagaattc ... tgttggacagGCTGTTCTCTTGTTCCAGAGAATAGAAGGTGTGGAAGTATGTCTATTTGGC
EST: gi|211490473|gb|FL383680.1|FL383680
EST:     AAATTTTTCAAGAAGACAACTACCCTACAGAGTTCCCTTACAAGTCCAAG                         GCTGTTCTCTTGTTCCAGAGAATAGAAGGTGTGGAAGTATGTCTATTTGGC
genomic: AAATTTTTCAAGAAGACAACTACCCTACAGAGTTCCCTTACAAGTCCAAGgtaagaattc ... tgttggacagGCTGTTCTCTTGTTCCAGAGAATAGAAGGTGTGGAAGTATGTCTATTTGGC
EST: gi|211539239|gb|FL396300.1|FL396300
EST:     AAATTTTTCAAGAAGACAACTACCCTACAGAGTTCCCTTACAAGTCCAAG                         GCTGTTCTCTTGTTCCAGAGAATAGAAGGTGTGGAAGTATGTCTATTTGGC
genomic: AAATTTTTCAAGAAGACAACTACCCTACAGAGTTCCCTTACAAGTCCAAGgtaagaattc ... tgttggacagGCTGTTCTCTTGTTCCAGAGAATAGAAGGTGTGGAAGTATGTCTATTTGGC
EST: gi|211179796|gb|FL384668.1|FL384668
EST:     AAATTTTTCAAGAAGACAACTACCCTACAGAGTTCCCTTACAAGTCCAAG                         GCTGTTCTCTTGTTCCAGAGAATANAAGGNGTGGAAGTATGTCTATTTGGC
genomic: AAATTTTTCAAGAAGACAACTACCCTACAGAGTTCCCTTACAAGTCCAAGgtaagaattc ... tgttggacagGCTGTTCTCTTGTTCCAGAGAATAGAAGGTGTGGAAGTATGTCTATTTGGC
EST: gi|211153694|gb|FL418631.1|FL418631
EST:     AAATTTTTCAAGAAGACAACTACCCTACAGAGTTCCCTTACAAGTCCAAG                         GCTGTTCTCTTGTTCCAGAGAATAGAAGGTGTGGAAGTATGTCTATTTGGC
genomic: AAATTTTTCAAGAAGACAACTACCCTACAGAGTTCCCTTACAAGTCCAAGgtaagaattc ... tgttggacagGCTGTTCTCTTGTTCCAGAGAATAGAAGGTGTGGAAGTATGTCTATTTGGC
EST: gi|211085796|gb|FL424018.1|FL424018
EST:     AAATTTTTCAAGAAGACAACTACCCTACAGAGTTCCCTTACAAGTCCAAG                         GCTGTTCTCTTGTTCCAGAGAATAGAAGGTGNGGAAGTATGTCTATTTGGC
genomic: AAATTTTTCAAGAAGACAACTACCCTACAGAGTTCCCTTACAAGTCCAAGgtaagaattc ... tgttggacagGCTGTTCTCTTGTTCCAGAGAATAGAAGGTGTGGAAGTATGTCTATTTGGC
EST: gi|211046001|gb|FL422502.1|FL422502
EST:     AAATTTTTCAAGAAGACAACTACCCTACAGAGTTCCCTTACAAGTCCAAG                         GCTGTTCTCTTGTTCCAGAGAATAGAAGGTGTGGAAGTATGTCTATTTGGC
genomic: AAATTTTTCAAGAAGACAACTACCCTACAGAGTTCCCTTACAAGTCCAAGgtaagaattc ... tgttggacagGCTGTTCTCTTGTTCCAGAGAATAGAAGGTGTGGAAGTATGTCTATTTGGC
EST: gi|211343346|gb|FL378210.1|FL378210
EST:     AAATTTTTCAAGAAGACAACTACCCTACAGAGTTCCCTTACAAGTCCAAG                         GCTGTTCTCTTGTTCCAGAGAATAGAAGGTGTGGAAGTATGTCTATTTGGC
genomic: AAATTTTTCAAGAAGACAACTACCCTACAGAGTTCCCTTACAAGTCCAAGgtaagaattc ... tgttggacagGCTGTTCTCTTGTTCCAGAGAATAGAAGGTGTGGAAGTATGTCTATTTGGC
EST: gi|211398119|gb|FL400636.1|FL400636
EST:     AAATTTTTCAAGAAGACAACTACCCTACAGAGTTCCCTTACAAGTCCAAG                         GCTGTTCTCTTGTTCCAGAGAATAGAAGGTGTGGAAGTATGTCTATTTGGC
genomic: AAATTTTTCAAGAAGACAACTACCCTACAGAGTTCCCTTACAAGTCCAAGgtaagaattc ... tgttggacagGCTGTTCTCTTGTTCCAGAGAATAGAAGGTGTGGAAGTATGTCTATTTGGC

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: 37 (upstream exon), 49 (downstream exon)
Score: 57

AGTTGTTTCATCAGTGGATAAAAAGCTGGAGGTTAAACCACGTTTTTTGGAAATTTTTCAAGAAGACAACTACCCTACAGAGTTCCCTTACAAGTCCAAGgtaagaattc ... tgttggacagGCTGTTCTCTTGTTCCAGAGAATAGAAGGTGTGGAAGTATGTCTATTTGGCATGTATGTTCAAGAATTTGGTGCAGAATGCTCTTCCCCGAACCAGCGCC


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 49

AGTTGTTTCATCAGTGGATAAAAAGCTGGAGGTTAAACCACGTTTTTTGGAAATTTTTCAAGAAGACAACTACCCTACAGAGTTCCCTTACAAGTCCAAGgtaagaattc ... tgttggacagGCTGTTCTCTTGTTCCAGAGAATAGAAGGTGTGGAAGTATGTCTATTTGGCATGTATGTTCAAGAATTTGGTGCAGAATGCTCTTCCCCGAACCAGCGCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 74

AGTTGTTTCATCAGTGGATAAAAAGCTGGAGGTTAAACCACGTTTTTTGGAAATTTTTCAAGAAGACAACTACCCTACAGAGTTCCCTTACAAGTCCAAGgtaagaattc ... tgttggacagGCTGTTCTCTTGTTCCAGAGAATAGAAGGTGTGGAAGTATGTCTATTTGGCATGTATGTTCAAGAATTTGGTGCAGAATGCTCTTCCCCGAACCAGCGCC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 61

AGTTGTTTCATCAGTGGATAAAAAGCTGGAGGTTAAACCACGTTTTTTGGAAATTTTTCAAGAAGACAACTACCCTACAGAGTTCCCTTACAAGTCCAAGgtaagaattc ... tgttggacagGCTGTTCTCTTGTTCCAGAGAATAGAAGGTGTGGAAGTATGTCTATTTGGCATGTATGTTCAAGAATTTGGTGCAGAATGCTCTTCCCCGAACCAGCGCC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGTTGTTTCATCAGTGGATAAAAAGCTGGAGGTTAAACCACGTTTTTTGGAAATTTTTCAAGAAGACAACTACCCTACAGAGTTCCCTTACAAGTCCAAGgtaagaattcattcttgtcatttgaagcatgaatcgtagttacactcactaatttctgcaacactattttttatgaaatgttggacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG