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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGACCTTGCGGCCGCCGCTGGTGGCGAGCGCCGTGGAGAGGACCACCTGCCGTTCCTCGAGATCTTCCAGAACACCAAACTCATGGCCTCGCCCGCGCAGgtgaggcttccgcgcttgtatcgtctgcgggaatggagctgctgttatttgttatgaggctggttgcggaaagaggggaaattatgggttgaactctttc...

Basic information

species Zea mays
transcript GRMZM2G030072_T02
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G030072_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os03g22430.1 (Oryza sativa), 5'ss of exon 1
GGACCTTGCGGCCGCCGCTGGTGGCGAGCGCCGTGGAGAGGACCACCTGCCGTTCCTCGAGATCTTCCAGAACACCAAACTCATGGCCTCGCCCGCGCAGgtga----ggcttccgcgctt---gtatcgtctgcgggaatggagctgctgttatttgttatgaggctggttgcggaaagaggggaaattatgggttgaactctttc
|  ||  || || || || ||||||| |||||| || || ||||||||||||||||||||||||||||||||| |||| |||||||||||||||||||||||||    ||     | | ||   ||    |    | ||| |     || |  |  ||  |||   ||| |  || |       | |||       |    |     
GCTCCAGGCTGCGGCGGCAGGTGGCGGGCGCCGCGGCGACGACCACCTGCCGTTCCTCGAGATCTTCCAGAACGCCAAGCTCATGGCCTCGCCCGCGCAGgtgattgggggggaggggtttcccgtgattttcctgcgaaagagttagccgaaacatgagatg---ctgatgccgtagtccatagcaatagcaacatagcgtt----
















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|211075821|gb|FL010807.1|FL010807
EST:     GTTCCTCGAGATCTTCCAGAACACCAAACTCATGGCCTCGCCCGGCGCAG                         GTGGAACGGTCTAGCAGCTCGTATAGTCAGCACAGACCTAGAAGGCCTCC
genomic: GTTCCTCGAGATCTTCCAGAACACCAAACTCATGGCCTCGCCCG-CGCAGgtgaggcttc ... taattgtcagGTGGAACGGTCTAGCAGCTCGTATAGTCAGCACAGACCTAGAAGGCCTCC
EST: gi|211112205|gb|FK971815.1|FK971815
EST:     CGTTCCTCGAGATCTTCCAGAACACCAAACTCATGGCCTCGCCCGCGCAG                         GTGGAACGGTC
genomic: CGTTCCTCGAGATCTTCCAGAACACCAAACTCATGGCCTCGCCCGCGCAGgtgaggcttc ... taattgtcagGTGGAACGGTC
EST: gi|211078556|gb|FL010811.1|FL010811
EST:     CGTTCCTCGAGATCTTCCAGAACACCAAACTCATGGCCTCGCCCGCGCAG                         GTGGAACGGTCTAGCAGCTCGTATAGTCAGCACAGACCTAGAAGGCCTCCT
genomic: CGTTCCTCGAGATCTTCCAGAACACCAAACTCATGGCCTCGCCCGCGCAGgtgaggcttc ... taattgtcagGTGGAACGGTCTAGCAGCTCGTATAGTCAGCACAGACCTAGAAGGCCTCCT
EST: gi|211078557|gb|FL010812.1|FL010812
EST:     CGTTCCTCGAGATCTTCCAGAACACCAAACTCATGGCCTCGCCCGCGCAG                         GTGGAACGGTCTAGCAGCTCGTATAGTCAGCACAGACCTAGAAGGCCTCCT
genomic: CGTTCCTCGAGATCTTCCAGAACACCAAACTCATGGCCTCGCCCGCGCAGgtgaggcttc ... taattgtcagGTGGAACGGTCTAGCAGCTCGTATAGTCAGCACAGACCTAGAAGGCCTCCT
EST: gi|211078559|gb|FL010814.1|FL010814
EST:     CGTTCCTCGAGATCTTCCAGAACACCAAACTCATGGCCTCGCCCGCGCAG                         GTGGAACGGTCTAGCAGCTCGTATAGTCAGCACAGACCTAGAAGGCCTCCT
genomic: CGTTCCTCGAGATCTTCCAGAACACCAAACTCATGGCCTCGCCCGCGCAGgtgaggcttc ... taattgtcagGTGGAACGGTCTAGCAGCTCGTATAGTCAGCACAGACCTAGAAGGCCTCCT
EST: gi|211078554|gb|FL010809.1|FL010809
EST:     CGTTCCTCGAGATCTTCCAGAACACCAAACTCATGGCCTCGCCCGCGCAG                         GTGGAACGGTCTAGCAGCTCGTATAGTCAGCACAGACCTAGAAGGC-TCCT
genomic: CGTTCCTCGAGATCTTCCAGAACACCAAACTCATGGCCTCGCCCGCGCAGgtgaggcttc ... taattgtcagGTGGAACGGTCTAGCAGCTCGTATAGTCAGCACAGACCTAGAAGGCCTCCT
EST: gi|211078562|gb|FL010817.1|FL010817
EST:     CGTTCCTCGAGATCTTCCAGAACAMCAAACTCATGGCCTCGCCCGCGCAR                         GTGGAACGGTCTAGCAGCTCGTATAGTCAGCACAG
genomic: CGTTCCTCGAGATCTTCCAGAACACCAAACTCATGGCCTCGCCCGCGCAGgtgaggcttc ... taattgtcagGTGGAACGGTCTAGCAGCTCGTATAGTCAGCACAG
EST: gi|87157696|gb|DY402485.1|DY402485
EST:     CGTTCCTCGAGATCTTCCAGAACACCAAACTCATGGCCTCGCCCGCGCAG                         GTGGAACGGTCTAGCAGCTCGTATAGTCAGCACAGACCTAGAAGGCCTCCT
genomic: CGTTCCTCGAGATCTTCCAGAACACCAAACTCATGGCCTCGCCCGCGCAGgtgaggcttc ... taattgtcagGTGGAACGGTCTAGCAGCTCGTATAGTCAGCACAGACCTAGAAGGCCTCCT
EST: gi|211078553|gb|FL010808.1|FL010808
EST:     CGTTCCTCGAGATCTTCCAGAACACCAAACTCATGGCCTCGCCCGCGCAG                         GTGGAACGGTCTAGCAGCTCGTATAGTCAGCACAGACCTAGAAGGCCTCCT
genomic: CGTTCCTCGAGATCTTCCAGAACACCAAACTCATGGCCTCGCCCGCGCAGgtgaggcttc ... taattgtcagGTGGAACGGTCTAGCAGCTCGTATAGTCAGCACAGACCTAGAAGGCCTCCT
EST: gi|211075819|gb|FL010805.1|FL010805
EST:     CGTTCCTCGAGATCTTCCAGAACACCAAACTCATGGCCTCGCCCGCGCAG                         GTGGAACGGTCTAGCAGCTCGTATAGTCAGCACA
genomic: CGTTCCTCGAGATCTTCCAGAACACCAAACTCATGGCCTCGCCCGCGCAGgtgaggcttc ... taattgtcagGTGGAACGGTCTAGCAGCTCGTATAGTCAGCACA
EST: gi|211075818|gb|FL010804.1|FL010804
EST:     CGTTCCTCGAGATCTTCCAGAACACCAAACTCATGGCCTCGCCCGCGCAG                         GTGGAACGGTCTAGCAGCTCGTATAGTCAGCACAGA
genomic: CGTTCCTCGAGATCTTCCAGAACACCAAACTCATGGCCTCGCCCGCGCAGgtgaggcttc ... taattgtcagGTGGAACGGTCTAGCAGCTCGTATAGTCAGCACAGA
EST: gi|22472811|gb|BU037291.1|BU037291
EST:     CGTTCCTCGAGATCTTCCAGAACACCAAACTCATGGCCTCGCCCGCGCAG                         GTGGAACGGTCTAGCAGCTCGTATAGTCAGCAACAGAC
genomic: CGTTCCTCGAGATCTTCCAGAACACCAAACTCATGGCCTCGCCCGCGCAGgtgaggcttc ... taattgtcagGTGGAACGGTCTAGCAGCTCGTATAGTCAGCA-CAGAC
EST: gi|211078561|gb|FL010816.1|FL010816
EST:     CGTTCCTCGAGATCTTCCAGAACACCAAACTCATGGCCTCGCC-GCGCAG                         GTGGAACGGTCTAGCAGCTCGTATAGTCAGCACAGACCTAGAAGGCCTCCT
genomic: CGTTCCTCGAGATCTTCCAGAACACCAAACTCATGGCCTCGCCCGCGCAGgtgaggcttc ... taattgtcagGTGGAACGGTCTAGCAGCTCGTATAGTCAGCACAGACCTAGAAGGCCTCCT
EST: gi|26558842|gb|CA831077.1|CA831077
EST:     CGTTCCTCGAGATCTTCCAGAACACCAAACTCATGGCCTCGCCCGCGCAG                         GTGGAACGGTCTAGCAGCTCGTATAGTCAGCACAGACCTAGAAGGCCTCCT
genomic: CGTTCCTCGAGATCTTCCAGAACACCAAACTCATGGCCTCGCCCGCGCAGgtgaggcttc ... taattgtcagGTGGAACGGTCTAGCAGCTCGTATAGTCAGCACAGACCTAGAAGGCCTCCT
EST: gi|211075820|gb|FL010806.1|FL010806
EST:     CGTTCCTCGAGATCTTCCATAACACCAAACTCATGGCCTCGCCCGCGCAG                         GTGGAACGGTCTAGCAGCTCGTATAGTCAGCACAGACCTAGAAGG
genomic: CGTTCCTCGAGATCTTCCAGAACACCAAACTCATGGCCTCGCCCGCGCAGgtgaggcttc ... taattgtcagGTGGAACGGTCTAGCAGCTCGTATAGTCAGCACAGACCTAGAAGG

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: 13

GGACCTTGCGGCCGCCGCTGGTGGCGAGCGCCGTGGAGAGGACCACCTGCCGTTCCTCGAGATCTTCCAGAACACCAAACTCATGGCCTCGCCCGCGCAGgtgaggcttc ... taattgtcagGTGGAACGGTCTAGCAGCTCGTATAGTCAGCACAGACCTAGAAGGCCTCCTCCAGATTTGCCTTCATTGCTTCTTCACGGCCGAATCGTTTATATTGGCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 25

GGACCTTGCGGCCGCCGCTGGTGGCGAGCGCCGTGGAGAGGACCACCTGCCGTTCCTCGAGATCTTCCAGAACACCAAACTCATGGCCTCGCCCGCGCAGgtgaggcttc ... taattgtcagGTGGAACGGTCTAGCAGCTCGTATAGTCAGCACAGACCTAGAAGGCCTCCTCCAGATTTGCCTTCATTGCTTCTTCACGGCCGAATCGTTTATATTGGCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 17

GGACCTTGCGGCCGCCGCTGGTGGCGAGCGCCGTGGAGAGGACCACCTGCCGTTCCTCGAGATCTTCCAGAACACCAAACTCATGGCCTCGCCCGCGCAGgtgaggcttc ... taattgtcagGTGGAACGGTCTAGCAGCTCGTATAGTCAGCACAGACCTAGAAGGCCTCCTCCAGATTTGCCTTCATTGCTTCTTCACGGCCGAATCGTTTATATTGGCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 18

GGACCTTGCGGCCGCCGCTGGTGGCGAGCGCCGTGGAGAGGACCACCTGCCGTTCCTCGAGATCTTCCAGAACACCAAACTCATGGCCTCGCCCGCGCAGgtgaggcttc ... taattgtcagGTGGAACGGTCTAGCAGCTCGTATAGTCAGCACAGACCTAGAAGGCCTCCTCCAGATTTGCCTTCATTGCTTCTTCACGGCCGAATCGTTTATATTGGCA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGACCTTGCGGCCGCCGCTGGTGGCGAGCGCCGTGGAGAGGACCACCTGCCGTTCCTCGAGATCTTCCAGAACACCAAACTCATGGCCTCGCCCGCGCAGgtgaggcttccgcgcttgtatcgtctgcgggaatggagctgctgttatttgttatgaggctggttgcggaaagaggggaaattatgggttgaactctttc

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