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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaataaaattcagtattatgagtagcattatagctcaagcctttaaattgtaaaatcctcgtgttaatcatcgatataattttaatggtaattattgtcgctgacctaatataccttcttcaatagTGCGAATTCTGCTGCTGTGGCCATTACAACTACAGACCTTGTTAGCAAGAGCATTGCTGTCCAGACTGAG

Basic information

species Zea mays
transcript GRMZM2G044237_T02
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G044237_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os03g17120.2 (Oryza sativa), 3'ss of exon 7
gtaataaaattcagtattatgagtagcattatagctcaagcctttaaattgtaaaatcctcgtgttaatcatcgatataattttaatggtaattattgtcgctgacctaatataccttcttcaat---agTGCGAATTCTGCTGCTGTGGCCATTACAACTACAGACCTTGTTAGCAAGAGCATTGCTGTCCAGACTGAG
                             ||||| |    |   |    |||||||| |   ||  | |        | ||||  ||    || | | |  || || || ||   || |  |  |   ||||| |||||||| ||||||||||||||||||||||||||||||||||||||||| ||||| ||||| |||
----------------------------gtatagttagcacgcattgcatgtaaaatgcatctgcaagt-------gtcatttctat----atgactatatctaacttattacctctgcccctgtcacagTGCAAATTCTGCAGCTGTGGCCATTACAACTACAGACCTTGTTAGCAAGAGCATCGCTGTACAGACAGAG

upper sequence: GRMZM2G044237_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA13G19450.1 (Glycine max), 3'ss of exon 8
gtaataaaattcagtattatgagtagcattatagctcaagcctttaaattgtaaaatcctcgtgttaatcatcgatataattttaatggtaattattgtcgctgacctaatataccttcttcaat--agTGCGAATTCTGCTGCTGTGGCCATTACAACTACAGACCTTGTTAGCAAGAGCATTGCTGTCCAGACTGAG
                            |  |  || ||  |||| ||  ||| |   |||     ||   | | | |   | || |  | |||  | |      |  |   ||    |||  ||  || ||  ||||||| |||||||| || || |||||||| ||||||||||||||  | ||  |  || ||  |
--------------------------tttggtttcttaa-tctttgaaaagtatatagctctgaacaacacttgctgtg--tctacttttcattccttttttcatcaaatcttattagcttgcattcagGGCAGATTCTGCAGCTGTGGCAATCACCACTACAGATCTTGTTAGCAAGAGTGTGGCAATTGAGTCTCTG
















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|71298836|gb|DR785405.1|DR785405
EST:     TTAAATTCACTACCTAGACTTGTGGGCTCACTGTCTTCTTCAGTTCAGGG                         TGCGAATTCTGCTGCTGTGGCCATTACAACTACAGACCTTGGTAGCAAGAG
genomic: TTAAATTCACTACCTAGACTTGTGGGCTCACTGTCTTCTTCAGTTCAGGGgtaataaaat ... tcttcaatagTGCGAATTCTGCTGCTGTGGCCATTACAACTACAGACCTTGTTAGCAAGAG
EST: gi|149095151|gb|EE180766.2|EE180766
EST:     TTAAATTCACTACCTAGACTTGTGGGCTCACTGTCTTCTTCAGTTCAGGG                         TGCGAATTCTGCTGCTGTGGGCATTACAACTACAGACCTTGTTAGCAAGAG
genomic: TTAAATTCACTACCTAGACTTGTGGGCTCACTGTCTTCTTCAGTTCAGGGgtaataaaat ... tcttcaatagTGCGAATTCTGCTGCTGTGGCCATTACAACTACAGACCTTGTTAGCAAGAG
EST: gi|148956344|gb|EC902151.2|EC902151
EST:     TTAAATTCACTACCTAGACTTGTGGGCTCACTGTCTTCTTCAGTTCAGGG                         TGCGAATTCTGCTGCTGTGGCCATTACAACTACAGACCTTGTTAGCAAGAG
genomic: TTAAATTCACTACCTAGACTTGTGGGCTCACTGTCTTCTTCAGTTCAGGGgtaataaaat ... tcttcaatagTGCGAATTCTGCTGCTGTGGCCATTACAACTACAGACCTTGTTAGCAAGAG
EST: gi|148938791|gb|EC883128.2|EC883128
EST:     TTAAATTCACTACCTAGACTTGTGGGCTCACTGTCTTCTTCAGTTCAGGG                         TGCGAATTCTGCTGCTGTGGCCATTACAACTACAGACCTTGTTAGCAAGAG
genomic: TTAAATTCACTACCTAGACTTGTGGGCTCACTGTCTTCTTCAGTTCAGGGgtaataaaat ... tcttcaatagTGCGAATTCTGCTGCTGTGGCCATTACAACTACAGACCTTGTTAGCAAGAG
EST: gi|78092275|gb|DV520649.1|DV520649
EST:     TTAAATTCACTACCTAGACTTGTGGGCTCACTGTCTTCTTCAGTTCAGGG                         TGCGAATTCTGCTGCTGTGGCCATTACAACTACAGACCTTGTTAGCAAGAG
genomic: TTAAATTCACTACCTAGACTTGTGGGCTCACTGTCTTCTTCAGTTCAGGGgtaataaaat ... tcttcaatagTGCGAATTCTGCTGCTGTGGCCATTACAACTACAGACCTTGTTAGCAAGAG
EST: gi|149009106|gb|EE041258.2|EE041258
EST:     TTAAATTCACTACCTACACTTGTGGGCTCACTGTCTTCTTCAGTTCACGG                         TGCGAATTCTGCTGCTGTGGCCATTACAACTACAGACCTTGTTAGCAAGAG
genomic: TTAAATTCACTACCTAGACTTGTGGGCTCACTGTCTTCTTCAGTTCAGGGgtaataaaat ... tcttcaatagTGCGAATTCTGCTGCTGTGGCCATTACAACTACAGACCTTGTTAGCAAGAG
EST: gi|148932140|gb|EC875563.2|EC875563
EST:     TTAAATTCACTACCTAGACTTGTGGGCTCACTGTCTTCTTCAGTTCAGGG                         TGCGAATTCTGCTGCTGTGGCCATTACAACTACAGACCTTGTTAGCAAGAG
genomic: TTAAATTCACTACCTAGACTTGTGGGCTCACTGTCTTCTTCAGTTCAGGGgtaataaaat ... tcttcaatagTGCGAATTCTGCTGCTGTGGCCATTACAACTACAGACCTTGTTAGCAAGAG
EST: gi|71446471|gb|DR827521.1|DR827521
EST:     TTAAATTCACTACCTAGACTTGTGGGCTCACTGTCTTCTTCAGTTCAGGG                         TGCGAATTCTGCTGCT
genomic: TTAAATTCACTACCTAGACTTGTGGGCTCACTGTCTTCTTCAGTTCAGGGgtaataaaat ... tcttcaatagTGCGAATTCTGCTGCT
EST: gi|148972816|gb|EE023801.2|EE023801
EST:     TTAAATTCACTACCTAGACTTGTGGGCTCACTGTCTTCTTCAGTTCAGGG                         TGCGAATTCTGCTGCTGTGGCCAT-ACAACTACAGACCTTGTTAGCAAGAG
genomic: TTAAATTCACTACCTAGACTTGTGGGCTCACTGTCTTCTTCAGTTCAGGGgtaataaaat ... tcttcaatagTGCGAATTCTGCTGCTGTGGCCATTACAACTACAGACCTTGTTAGCAAGAG
EST: gi|149110343|gb|EE190365.2|EE190365
EST:     TTAAATTCACTACCTAGACTTGTGGGCTCACTGTCTTCTTCAGTTCAGGG                         TGCGAATTCTGCTGCTGTGGTCATTACAACTACAGACCTTGTTAGCAAGAG
genomic: TTAAATTCACTACCTAGACTTGTGGGCTCACTGTCTTCTTCAGTTCAGGGgtaataaaat ... tcttcaatagTGCGAATTCTGCTGCTGTGGCCATTACAACTACAGACCTTGTTAGCAAGAG
EST: gi|60348874|gb|DN215847.1|DN215847
EST:     TTAAATTCACTACCTAGACTTGTGGGCTCACTGTCTTCTTCAGTTCAGGG                         TGCGAATTCTGCTGCTGTGGCCATTACAACTACAGACCTTGTTAGCAAGAG
genomic: TTAAATTCACTACCTAGACTTGTGGGCTCACTGTCTTCTTCAGTTCAGGGgtaataaaat ... tcttcaatagTGCGAATTCTGCTGCTGTGGCCATTACAACTACAGACCTTGTTAGCAAGAG

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: 293

GAGGCACTTTTAAATTCACTACCTAGACTTGTGGGCTCACTGTCTTCTTCAGTTCAGGGgtaataaaat ... tcttcaatagTGCGAATTCTGCTGCTGTGGCCATTACAACTACAGACCTTGTTAGCAAGAGCATTGCTGTCCAGACTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 281

GAGGCACTTTTAAATTCACTACCTAGACTTGTGGGCTCACTGTCTTCTTCAGTTCAGGGgtaataaaat ... tcttcaatagTGCGAATTCTGCTGCTGTGGCCATTACAACTACAGACCTTGTTAGCAAGAGCATTGCTGTCCAGACTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 223

GAGGCACTTTTAAATTCACTACCTAGACTTGTGGGCTCACTGTCTTCTTCAGTTCAGGGgtaataaaat ... tcttcaatagTGCGAATTCTGCTGCTGTGGCCATTACAACTACAGACCTTGTTAGCAAGAGCATTGCTGTCCAGACTGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 158

GAGGCACTTTTAAATTCACTACCTAGACTTGTGGGCTCACTGTCTTCTTCAGTTCAGGGgtaataaaat ... tcttcaatagTGCGAATTCTGCTGCTGTGGCCATTACAACTACAGACCTTGTTAGCAAGAGCATTGCTGTCCAGACTGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgatataattttaatggtaattattgtcgctgacctaatataccttcttcaatagTGCGAATTCTGCTGCTGTGGCCATTACAACTACAGACCTTGTTAGCAAGAGCATTGCTGTCCAGACTGAG
                                acctaat  putative branch site (score: 158)
                                        taccttcttc  CT-rich tract
     taattttaatggtaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaataaaattcagtattatgagtagcattatagctcaagcctttaaattgtaaaatcctcgtgttaatcatcgatataattttaatggtaattattgtcgctgacctaatataccttcttcaatagTGCGAATTCTGCTGCTGTGGCCATTACAACTACAGACCTTGTTAGCAAGAGCATTGCTGTCCAGACTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA