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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgggaacagtagcactgaacaattatatggttttactttattttctctcttattaatcggtggcaatttgcgatatataacttatgctgcagTTTGAGGCTGCATGGGCACTCACCAACATTGCATCAGGCACATCAGAGAACACTAAGGTGGTCGTTGAGAGTGGTGCTGTGCCCATCTTTGTCAAGCTAC

Basic information

species Zea mays
transcript GRMZM2G468150_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G468150_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os05g06350.1 (Oryza sativa), 3'ss of exon 3
gtctgggaacagtagcactgaacaattatatggttttactttattttc--tctcttattaatcggtggcaatttgcgatatataacttatgctgcagTTTGAGGCTGCATGGGCACTCACCAACATTGCATCAGGCACATCAGAGAACACTAAGGTGGTCGTTGAGAGTGGTGCTGTGCCCATCTTTGTCAAGCTAC
|| || |||||| || ||| | | || | || | | | || ||| | | | || | || | || | ||||||||||||||||||||||||||| ||||||||||||||||||||||| ||||| || ||||| |||||| |||||||||||||||||||||||| || |
gtgtgtcaacagtcacagtgatttaatttactaatagtgttaactaggaaccatttgctaaa-gctaaccatcccccatgggt--tttcttgcgcagTTTGAGGCTGCATGGGCACTCACTAACATTGCATCAGGCACATCAGATAACACCAAAGTGGTAGTTGAGTCTGGTGCTGTGCCCATCTTTGTCAAACTGC

upper sequence: GRMZM2G468150_T01 (Zea mays), 3'ss of exon 2
lower sequence: EDO99338 (Chlamydomonas reinhardtii), 3'ss of exon 3
gtctgggaacagtagcactgaacaat----tatatggttttac-tttattttctctcttattaatcggtggcaatttgc---gatatataacttatgctgc----agTTTGAGGCTGCATGGGCACTCACCAACATTGCATCAGGCACATCAGAGAACACTAAGGTGGTCGTTGAGAGTGGTGCTGTGCCCATCTTTGTCAAGCTAC
|| | | | ||||| || | |||| || | ||||| || | ||| | || | || | || |||| ||||||||||||| ||||| ||||||||| | || || ||||| || ||| |||| |||||||| | || || |||||||| ||||| |||| |
gttggcgtggggccgcactcgcagatgttgcacttggtcttgcatttatccgtgtcattgcctgtatgtg-tagttcgtttaagcggttatttcatactgctaacagTTTGAGGCTGCGTGGGCGCTCACCAACGTCGCGTCGGGCACCTCGGAGCACACGAAGGTGGTTATCGACCACAACGCGGTGCCCATTTTTGTTCAGCTGC
















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|60394006|gb|DN226876.1|DN226876
EST:     TGCCGCGATTCATTGAGTTTCTTACACGTGAGGACCATCCCCAACTCCAG                         TTTGAGGCTGCATGGGCACTCACCAACATTGCATCAGGCACATCAGAGAAC
genomic: TGCCGCGATTCATTGAGTTTCTTACACGTGAGGACCATCCCCAACTCCAGgtctgggaac ... tatgctgcagTTTGAGGCTGCATGGGCACTCACCAACATTGCATCAGGCACATCAGAGAAC
EST: gi|18163824|gb|BM333663.1|BM333663
EST:     TGCCGCGATTCATTGAGTTTCTTACACGTGAGGACCATCCCCAACTCCAG                         TTTGAGGCTGCATGGGCACTCACCAACATTGCATCAGGCACATCAGAGAAC
genomic: TGCCGCGATTCATTGAGTTTCTTACACGTGAGGACCATCCCCAACTCCAGgtctgggaac ... tatgctgcagTTTGAGGCTGCATGGGCACTCACCAACATTGCATCAGGCACATCAGAGAAC
EST: gi|71446169|gb|DR827219.1|DR827219
EST:     TGCCGCGATTCATTGAGTTTCTTACACGTGAGGACCATCCCCAACTCCAG                         TTTGAGGCTGCATGGGCACTCACCAACATTGCATCAGGCACATCAGA-A-C
genomic: TGCCGCGATTCATTGAGTTTCTTACACGTGAGGACCATCCCCAACTCCAGgtctgggaac ... tatgctgcagTTTGAGGCTGCATGGGCACTCACCAACATTGCATCAGGCACATCAGAGAAC
EST: gi|60349448|gb|DN216421.1|DN216421
EST:     TGCCGCGATTCATTGAGTTTCTTACACGTGAGGACCATCCCCAACTCCAG                         TTTGAGGCTGCATGGGCACTCACCAACATTGCATCAGGCACATCAGAGAAC
genomic: TGCCGCGATTCATTGAGTTTCTTACACGTGAGGACCATCCCCAACTCCAGgtctgggaac ... tatgctgcagTTTGAGGCTGCATGGGCACTCACCAACATTGCATCAGGCACATCAGAGAAC
EST: gi|71446170|gb|DR827220.1|DR827220
EST:     TGCCGCGATTCATTGAGTTTCTTACACGTGAGGACCATCCCCAACTCCAG                         TTTGAGGCTGCATGGGCACTCACCAACATTGCATCAGGCACATC--AGAAC
genomic: TGCCGCGATTCATTGAGTTTCTTACACGTGAGGACCATCCCCAACTCCAGgtctgggaac ... tatgctgcagTTTGAGGCTGCATGGGCACTCACCAACATTGCATCAGGCACATCAGAGAAC

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), 45 (downstream exon)
Score: 12

TCCCCCCAATCGAAGAGGTGATCAGCACAGGAGTGGTGCCGCGATTCATTGAGTTTCTTACACGTGAGGACCATCCCCAACTCCAGgtctgggaac ... tatgctgcagTTTGAGGCTGCATGGGCACTCACCAACATTGCATCAGGCACATCAGAGAACACTAAGGTGGTCGTTGAGAGTGGTGCTGTGCCCATCTTTGTCAAGCTAC


Block sizes: 43 (upstream exon), 48 (downstream exon)
Score: 13

TCCCCCCAATCGAAGAGGTGATCAGCACAGGAGTGGTGCCGCGATTCATTGAGTTTCTTACACGTGAGGACCATCCCCAACTCCAGgtctgggaac ... tatgctgcagTTTGAGGCTGCATGGGCACTCACCAACATTGCATCAGGCACATCAGAGAACACTAAGGTGGTCGTTGAGAGTGGTGCTGTGCCCATCTTTGTCAAGCTAC


Block sizes: 25 (upstream exon), 42 (downstream exon)
Score: 5

TCCCCCCAATCGAAGAGGTGATCAGCACAGGAGTGGTGCCGCGATTCATTGAGTTTCTTACACGTGAGGACCATCCCCAACTCCAGgtctgggaac ... tatgctgcagTTTGAGGCTGCATGGGCACTCACCAACATTGCATCAGGCACATCAGAGAACACTAAGGTGGTCGTTGAGAGTGGTGCTGTGCCCATCTTTGTCAAGCTAC


Block sizes: 27 (upstream exon), 23 (downstream exon)
Score: 3

TCCCCCCAATCGAAGAGGTGATCAGCACAGGAGTGGTGCCGCGATTCATTGAGTTTCTTACACGTGAGGACCATCCCCAACTCCAGgtctgggaac ... tatgctgcagTTTGAGGCTGCATGGGCACTCACCAACATTGCATCAGGCACATCAGAGAACACTAAGGTGGTCGTTGAGAGTGGTGCTGTGCCCATCTTTGTCAAGCTAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttattttctctcttattaatcggtggcaatttgcgatatataacttatgctgcagTTTGAGGCTGCATGGGCACTCACCAACATTGCATCAGGCACATCAGAGAACACTAAGGTGGTCGTTGAGAGTGGTGCTGTGCCCATCTTTGTCAAGCTAC
                                   atatataacttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctgggaacagtagcactgaacaattatatggttttactttattttctctcttattaatcggtggcaatttgcgatatataacttatgctgcagTTTGAGGCTGCATGGGCACTCACCAACATTGCATCAGGCACATCAGAGAACACTAAGGTGGTCGTTGAGAGTGGTGCTGTGCCCATCTTTGTCAAGCTAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT