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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacctgaaataacctgtttccttcgtctgaaatgcttgcactcccttccatggtgctccttgaaccgcatcaacgaatcatggctccatgaatataataaatatcagGAATGGATCAGCCTGGAAACCTCACGCGCGAGGAGTACGTGCACGACGCCGTGAGGATCGACTTCTACAAGAACTACCTGACGGAGCTAAAGAGAGGGAT

Basic information

species Zea mays
transcript AC217401.3_FGT002
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC217401.3_FGT002 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os03g49610.1 (Oryza sativa), 3'ss of exon 10
gtacctgaaataacctgtttccttcgtctgaaatgcttgcactcccttccatggtgctccttgaaccgcatcaacgaatcatggctccatgaatataataa--atatcagGAATGGATCAGCCTGGAAACCTCACGCGCGAGGAGTACGTGCACGACGCCGTGAGGATCGACTTCTACAAGAACTACCTGACGGAGCTAAAGAGAGGGAT
                                ||  |   ||| |||  | | ||  |  || ||     || | | ||         |    |||  | |   || |||||||||||||  ||||||| ||||| || || |||| | |||| ||| |||  ||||| || ||||||||||||||||| || || || |||| ||  ||
------------------------------gtattttcaaactacctatc-tagttttaattcaaaattttccatgcatttctcaaaaaaatttatggtcatggtaccagGAATGGATCAATCTGGAAATCTCACTCGTGAAGAGTTCCTGCATGACACCGAAAGGATTGAGTTCTACAAGAACTACCTCACTGAACTGAAGAAAGCCAT
















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|211180527|gb|FL077087.1|FL077087
EST:     CATATCGGAAAACG                         GAATGGATCAGCCTGGAAACCTCACGCGCGAGGAGTACGTGCACGACGCCG
genomic: CATATCGGAAAACGgtacctgaaa ... taaatatcagGAATGGATCAGCCTGGAAACCTCACGCGCGAGGAGTACGTGCACGACGCCG
EST: gi|211180529|gb|FL077089.1|FL077089
EST:     CATATCGGAAAACG                         GAATGGATCAGCCTGGAAACCTCACGCGCGAGGAGTACGTGCACGACGCCG
genomic: CATATCGGAAAACGgtacctgaaa ... taaatatcagGAATGGATCAGCCTGGAAACCTCACGCGCGAGGAGTACGTGCACGACGCCG
EST: gi|32856217|gb|CD995898.1|CD995898
EST:     CTACCTAAAGGAAAAGGACCATAATCCAATCATCATCATATCGGAAAACG                         GAATGGATCAGCCTGGAAACCTCACGCGCGAGGAGTACGTGCACGACGCCG
genomic: CTACCTAAAGGAAAAGTACCATAATCCAATCATCATCATATCGGAAAACGgtacctgaaa ... taaatatcagGAATGGATCAGCCTGGAAACCTCACGCGCGAGGAGTACGTGCACGACGCCG
EST: gi|211180526|gb|FL077086.1|FL077086
EST:     ATCGGAAAACG                         GAATGGATCAGCCTGGAAACCTCACGCGCGAGGAGTACGTGCACGACGCCG
genomic: ATCGGAAAACGgtacctgaaa ... taaatatcagGAATGGATCAGCCTGGAAACCTCACGCGCGAGGAGTACGTGCACGACGCCG
EST: gi|5525221|gb|AI861219.1|AI861219
EST:     CTACCTAAAGGAAAAGTACCATAATCCAATCATCATCATATCGGAAAACG                         GAATGGATCAGCCTGGAAACCTCACGCNCGAGGAGTACGTGCNCGACGCCG
genomic: CTACCTAAAGGAAAAGTACCATAATCCAATCATCATCATATCGGAAAACGgtacctgaaa ... taaatatcagGAATGGATCAGCCTGGAAACCTCACGCGCGAGGAGTACGTGCACGACGCCG
EST: gi|67013218|gb|CO441967.1|CO441967
EST:     CTACCTAAAGGAAAAGTACCATAATCCAATCATCATCATATCGGAAAACG                         GAATGGATCAGCCTGGAAACCTCACGCGCGAGGAGTACGTGCACGACGCCG
genomic: CTACCTAAAGGAAAAGTACCATAATCCAATCATCATCATATCGGAAAACGgtacctgaaa ... taaatatcagGAATGGATCAGCCTGGAAACCTCACGCGCGAGGAGTACGTGCACGACGCCG
EST: gi|211180531|gb|FL077091.1|FL077091
EST:     CATATCGGAAAACG                         GAATGGATCAGCCTGGAAACCTCACGCGCGAGGAGTACGTGCACGACGCCG
genomic: CATATCGGAAAACGgtacctgaaa ... taaatatcagGAATGGATCAGCCTGGAAACCTCACGCGCGAGGAGTACGTGCACGACGCCG
EST: gi|60341656|gb|DN208629.1|DN208629
EST:     CTACCTAAAGGAAAAGTACCATAATCCAATCATCATCATATCGGAAAACG                         GAATGGATCAGCCTGGAAACCTCACGCGCGAGGAGTACGTGCACGACGCCG
genomic: CTACCTAAAGGAAAAGTACCATAATCCAATCATCATCATATCGGAAAACGgtacctgaaa ... taaatatcagGAATGGATCAGCCTGGAAACCTCACGCGCGAGGAGTACGTGCACGACGCCG
EST: gi|78075435|gb|DV503869.1|DV503869
EST:     CTACCTAAAGGAAAAGTACCATAATCCAATCATCATCATATCGGAAAACG                         GAATGGATCAGCCTGGAAACCTCACGCGCGAGGAGTACGTGCACGACGCCG
genomic: CTACCTAAAGGAAAAGTACCATAATCCAATCATCATCATATCGGAAAACGgtacctgaaa ... taaatatcagGAATGGATCAGCCTGGAAACCTCACGCGCGAGGAGTACGTGCACGACGCCG
EST: gi|60343713|gb|DN210686.1|DN210686
EST:     CTACCTAAAGGAAAAGTACCATAATCCAATCATCATCATATCGGAAAACG                         GAATGGATCAGCCTGGAAACCTCACGCGCGAGGAGTACGTGCACGACGCCG
genomic: CTACCTAAAGGAAAAGTACCATAATCCAATCATCATCATATCGGAAAACGgtacctgaaa ... taaatatcagGAATGGATCAGCCTGGAAACCTCACGCGCGAGGAGTACGTGCACGACGCCG
EST: gi|211180528|gb|FL077088.1|FL077088
EST:     CATATCGGAAAACG                         GAATGGATCAGCCTGGAAACCTCACGCGCGAGGAGTACGTGCACGACGCCG
genomic: CATATCGGAAAACGgtacctgaaa ... taaatatcagGAATGGATCAGCCTGGAAACCTCACGCGCGAGGAGTACGTGCACGACGCCG
EST: gi|211180530|gb|FL077090.1|FL077090
EST:     CATATCGGAAAACG                         GAATGGATCAGCCTGGAAACCTCACGCGCGAGGAGTACGTGCACGACGCCG
genomic: CATATCGGAAAACGgtacctgaaa ... taaatatcagGAATGGATCAGCCTGGAAACCTCACGCGCGAGGAGTACGTGCACGACGCCG
EST: gi|78022826|gb|DV491213.1|DV491213
EST:     CTACCTAAAGGAAAAGTACCATAATCCAATCATCATCATATCGGAAAACG                         GAATGGATCAGCCTGGAAACCTCACGCGCGAGGAGTACGTGCACGACGCCG
genomic: CTACCTAAAGGAAAAGTACCATAATCCAATCATCATCATATCGGAAAACGgtacctgaaa ... taaatatcagGAATGGATCAGCCTGGAAACCTCACGCGCGAGGAGTACGTGCACGACGCCG
EST: gi|60351674|gb|DN218647.1|DN218647
EST:     CTACCTAAAGGAAAAGTACCATAATCCAATCATCATCATATCGGAAAACG                         GAATGGATCAGCCTGGAAACCTCACGCGCGAGGAGTACGTGCACGACGCCG
genomic: CTACCTAAAGGAAAAGTACCATAATCCAATCATCATCATATCGGAAAACGgtacctgaaa ... taaatatcagGAATGGATCAGCCTGGAAACCTCACGCGCGAGGAGTACGTGCACGACGCCG
EST: gi|60340042|gb|DN207015.1|DN207015
EST:     CTACCTAAAGGAAAAGTACCATAATCCAATCATCATCATATCGGAAAACG                         GAATGGATCAGCCTGGAAACCTCACGCGCGAGGAGTACGTGCACGACGCCG
genomic: CTACCTAAAGGAAAAGTACCATAATCCAATCATCATCATATCGGAAAACGgtacctgaaa ... taaatatcagGAATGGATCAGCCTGGAAACCTCACGCGCGAGGAGTACGTGCACGACGCCG
EST: gi|60352866|gb|DN219839.1|DN219839
EST:     CTACCTAAAGGAAAAGTACCATAATCCAATCATCATCATATCGGAAAACG                         GAATGGATCAGCCTGGAAACCTCACGCGCGAGGAGTACGTGCACGACGCCG
genomic: CTACCTAAAGGAAAAGTACCATAATCCAATCATCATCATATCGGAAAACGgtacctgaaa ... taaatatcagGAATGGATCAGCCTGGAAACCTCACGCGCGAGGAGTACGTGCACGACGCCG
EST: gi|60394083|gb|DN226953.1|DN226953
EST:     CTACCTAAAGGAAAAGTACCATAATCCAATCATCATCATATCGGAAAACG                         GAATGGATCAGCCTGGAAACCTCACGCGCGAGGAGTACGTGCACGACGCCG
genomic: CTACCTAAAGGAAAAGTACCATAATCCAATCATCATCATATCGGAAAACGgtacctgaaa ... taaatatcagGAATGGATCAGCCTGGAAACCTCACGCGCGAGGAGTACGTGCACGACGCCG
EST: gi|149014536|gb|EE044170.2|EE044170
EST:     CTACCTAAAGGAAAAGTACCATAATCCAATCATCATCATATCGGAAAACG                         GAATGGATCAGCCTGGAAACCTCACGCGCGAGGAGTACGTGCACGACGCCG
genomic: CTACCTAAAGGAAAAGTACCATAATCCAATCATCATCATATCGGAAAACGgtacctgaaa ... taaatatcagGAATGGATCAGCCTGGAAACCTCACGCGCGAGGAGTACGTGCACGACGCCG
EST: gi|60358129|gb|DN225102.1|DN225102
EST:     CTACCTAAAGGAAAAGTACCATAATCCAATCATCATCATATCGGAAAACG                         GAATGGATCAGCCTGGAAACCTCACGCGCGAGGAGTACGTGCACGACGCCG
genomic: CTACCTAAAGGAAAAGTACCATAATCCAATCATCATCATATCGGAAAACGgtacctgaaa ... taaatatcagGAATGGATCAGCCTGGAAACCTCACGCGCGAGGAGTACGTGCACGACGCCG
EST: gi|211493767|gb|FL172983.1|FL172983
EST:     AAAGTACCATAATCCAATCATCATCATATCGGAAAACG                         GAATGGATCAGCCTGGAAACCTCACGCGCGAGGAGTACGTGCACGACGCCG
genomic: AAAGTACCATAATCCAATCATCATCATATCGGAAAACGgtacctgaaa ... taaatatcagGAATGGATCAGCCTGGAAACCTCACGCGCGAGGAGTACGTGCACGACGCCG
EST: gi|40336432|gb|CK370502.1|CK370502
EST:     CTACCTAAAGGAAAAGTACCATAATCCAATCATCATCATATCGGAAAACG                         GAATGGATCAGCCTGGAAACCTCACGCGCGAGGAGTACGTGCACGACGCCG
genomic: CTACCTAAAGGAAAAGTACCATAATCCAATCATCATCATATCGGAAAACGgtacctgaaa ... taaatatcagGAATGGATCAGCCTGGAAACCTCACGCGCGAGGAGTACGTGCACGACGCCG
EST: gi|78075434|gb|DV503868.1|DV503868
EST:     TAATCCAATCATCATCATATCGGAAAACG                         GAATGGATCAGCCTGGAAACCTCACGCGCGAGGAGTACGTGCACGACGCCG
genomic: TAATCCAATCATCATCATATCGGAAAACGgtacctgaaa ... taaatatcagGAATGGATCAGCCTGGAAACCTCACGCGCGAGGAGTACGTGCACGACGCCG
EST: gi|37393320|gb|CF633922.1|CF633922
EST:     CTACCTAAAGGAAAAGTACCATAATCCAATCATCATCATATCGGAAAACG                         GAATGGATCAGCCTGGAAACCTCACGCGCGAGGAGTACGTGCACGACGCCG
genomic: CTACCTAAAGGAAAAGTACCATAATCCAATCATCATCATATCGGAAAACGgtacctgaaa ... taaatatcagGAATGGATCAGCCTGGAAACCTCACGCGCGAGGAGTACGTGCACGACGCCG
EST: gi|60345028|gb|DN212001.1|DN212001
EST:     CTACCTAAAGGAAAAGTACCATAATCCAATCATCATCATATCGGAAAACG                         GAATGGATCAGCCTGGAAACCTCACGCGCGAGGAGTACGTGCACGACGCCG
genomic: CTACCTAAAGGAAAAGTACCATAATCCAATCATCATCATATCGGAAAACGgtacctgaaa ... taaatatcagGAATGGATCAGCCTGGAAACCTCACGCGCGAGGAGTACGTGCACGACGCCG
EST: gi|37391018|gb|CF632748.1|CF632748
EST:     CTACCTAAAGGAAAAGTACCATAATCCAATCATCATCATATCGGAAAACG                         GAATGGATCAGCCTGGAAACCTCACGCGCGAGGAGTACGTGCACGACGCCG
genomic: CTACCTAAAGGAAAAGTACCATAATCCAATCATCATCATATCGGAAAACGgtacctgaaa ... taaatatcagGAATGGATCAGCCTGGAAACCTCACGCGCGAGGAGTACGTGCACGACGCCG
EST: gi|20507721|gb|BQ279747.1|BQ279747
EST:     CTACCTAAAGGAAAAGTACCATAATCCAATCATCATCATATCGGAAAACG                         GAATGGATCAGCCTGGAAACCTCACGCGCGAGGAGTACGTGCACGACGCCG
genomic: CTACCTAAAGGAAAAGTACCATAATCCAATCATCATCATATCGGAAAACGgtacctgaaa ... taaatatcagGAATGGATCAGCCTGGAAACCTCACGCGCGAGGAGTACGTGCACGACGCCG

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: 148

CACTCAATTTGGCTTTACATCGTCCCATCGGGCATGTATGGAGTCGTGAACTACCTAAAGGAAAAGTACCATAATCCAATCATCATCATATCGGAAAACGgtacctgaaa ... taaatatcagGAATGGATCAGCCTGGAAACCTCACGCGCGAGGAGTACGTGCACGACGCCGTGAGGATCGACTTCTACAAGAACTACCTGACGGAGCTAAAGAGAGGGAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 81

CACTCAATTTGGCTTTACATCGTCCCATCGGGCATGTATGGAGTCGTGAACTACCTAAAGGAAAAGTACCATAATCCAATCATCATCATATCGGAAAACGgtacctgaaa ... taaatatcagGAATGGATCAGCCTGGAAACCTCACGCGCGAGGAGTACGTGCACGACGCCGTGAGGATCGACTTCTACAAGAACTACCTGACGGAGCTAAAGAGAGGGAT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 34

CACTCAATTTGGCTTTACATCGTCCCATCGGGCATGTATGGAGTCGTGAACTACCTAAAGGAAAAGTACCATAATCCAATCATCATCATATCGGAAAACGgtacctgaaa ... taaatatcagGAATGGATCAGCCTGGAAACCTCACGCGCGAGGAGTACGTGCACGACGCCGTGAGGATCGACTTCTACAAGAACTACCTGACGGAGCTAAAGAGAGGGAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 106

CACTCAATTTGGCTTTACATCGTCCCATCGGGCATGTATGGAGTCGTGAACTACCTAAAGGAAAAGTACCATAATCCAATCATCATCATATCGGAAAACGgtacctgaaa ... taaatatcagGAATGGATCAGCCTGGAAACCTCACGCGCGAGGAGTACGTGCACGACGCCGTGAGGATCGACTTCTACAAGAACTACCTGACGGAGCTAAAGAGAGGGAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgctccttgaaccgcatcaacgaatcatggctccatgaatataataaatatcagGAATGGATCAGCCTGGAAACCTCACGCGCGAGGAGTACGTGCACGACGCCGTGAGGATCGACTTCTACAAGAACTACCTGACGGAGCTAAAGAGAGGGAT
                                   atgaatataataaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacctgaaataacctgtttccttcgtctgaaatgcttgcactcccttccatggtgctccttgaaccgcatcaacgaatcatggctccatgaatataataaatatcagGAATGGATCAGCCTGGAAACCTCACGCGCGAGGAGTACGTGCACGACGCCGTGAGGATCGACTTCTACAAGAACTACCTGACGGAGCTAAAGAGAGGGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG