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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcatcatgtatatgtgctcccttccgtttcatatgacggcaaatcaatcccatatgttctcatagcatctgcatggacttattgtaaaacctattgcagGACTGCCTATGATGTGTCCATTAATGACGACTCTTGGCCAACAGAAGTGTTTGAGCTTGTCACTGGAGAGAAATCGAAGACATTGGAAAGGCTTGACCC

Basic information

species Zea mays
transcript GRMZM2G067476_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G067476_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g01307.1 (Oryza sativa), 3'ss of exon 1
------tgcatcatgtatatgtgctccct-tccgtttcatatgacggcaaatcaatcccatatgttctcatagcatctgcatggacttattgtaaaacctattgcagGACTGCCTATGATGTGTCCATTAATGACGACTCTTGGCCAACAGAAGTGTTTGAGCTTGTCACTGGAGAGAAATCGAAGACATTGGAAAGGCTTGACCC
         ||  || ||  ||   |  | ||  | | |||||| |||||  |||     ||| | | ||||| |     ||  ||| |  ||||||  |||||||| |||||||||||||||  ||||||||| ||  |||||||||  || |  |||||||||||| |||||||||  || |||||||||||||||||||||||
tcttttcctattttggattagtttactttctctatgtgatatgatggcaag-caactatgtatat-cacatagta-----ataaactgaccgtaaaatttattgcagAACTGCCTATGATGTGAGCATTAATGATGATACTTGGCCAAAGGAGGCATTTGAGCTTGTCTCTGGAGAGATGTCAAAGACATTGGAAAGGCTTGACCC

upper sequence: GRMZM2G067476_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g01307.2 (Oryza sativa), 3'ss of exon 1
tgcatcatgtatatgtgctcccttccgtttcatatgacggcaaatcaatcccatatgttctcatagcatctgcatggacttattgtaaaacctattgcagGACTGCCTATGATGTGTCCATTAATGACGACTCTTGGCCAACAGAAGTGTTTGAGCTTGTCACTGGAGAGAAATCGAAGACATTGGAAAGGCTTGACCC
                                                                         ||  ||| |  ||||||  |||||||| |||||||||||||||  ||||||||| ||  |||||||||  || |  |||||||||||| |||||||||  || |||||||||||||||||||||||
----------------------------------------------------------------------gtaataaactgaccgtaaaatttattgcagaactgcctatgatgtgagcattaatgatgatacttggccaaaggaggcatttgagcttgtctctggagagATGTCAAAGACATTGGAAAGGCTTGACCC
















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|16926595|gb|BM079663.1|BM079663
EST:     CCCTCGACCTCTACAACCAGGGATCCGC                         GACTGCCTATGATGTGTCCATTAATGACGACTCTTGGCCAACAGAAGTGTT
genomic: CCCTCGACCTCTACAACCAGGGATCCGCgtgagcaccg ... cctattgcagGACTGCCTATGATGTGTCCATTAATGACGACTCTTGGCCAACAGAAGTGTT
EST: gi|17932024|gb|BM268984.1|BM268984
EST:     ACCAGGGATCCGC                         GACTGCCTATGATGTGTCCATTAATGACGACTCTTGGCCAACAGAAGTGTT
genomic: ACCAGGGATCCGCgtgagcaccg ... cctattgcagGACTGCCTATGATGTGTCCATTAATGACGACTCTTGGCCAACAGAAGTGTT
EST: gi|148973350|gb|EE024440.2|EE024440
EST:     GGCGTCGAGCGCGTCGCTGTCTCCCTCGACCTCTACAACCAGGGATCCGC                         GACTGCCTATGATGTGTCCATTAATGACGACTCTTGGCCAACAGAAGTGTT
genomic: GGCGTCGAGCGCGTCGCTGTCTCCCTCGACCTCTACAACCAGGGATCCGCgtgagcaccg ... cctattgcagGACTGCCTATGATGTGTCCATTAATGACGACTCTTGGCCAACAGAAGTGTT
EST: gi|60400336|gb|DN233143.1|DN233143
EST:     GGCGTCGAGCGCGTCGCTGTCTCCCTCGACCTCTACAACCAGGGATCCGC                         GACTGCCTATGATGTGTCCATTAATGACGACTCTTGGCCAACAGAAGTGTT
genomic: GGCGTCGAGCGCGTCGCTGTCTCCCTCGACCTCTACAACCAGGGATCCGCgtgagcaccg ... cctattgcagGACTGCCTATGATGTGTCCATTAATGACGACTCTTGGCCAACAGAAGTGTT
EST: gi|18168234|gb|BM338074.1|BM338074
EST:     GCGTCGAGCGCGTCGCTGTCTCCCTCGACCTATACAACCAGGGATCCGC                         GACTGCCTATGATGTGTCCATTAATGACGACTCTTGGCCAACAGAAGTGTT
genomic: GCGTCGAGCGCGTCGCTGTCTCCCTCGACCTCTACAACCAGGGATCCGCgtgagcaccg ... cctattgcagGACTGCCTATGATGTGTCCATTAATGACGACTCTTGGCCAACAGAAGTGTT
EST: gi|50331163|gb|CO526289.1|CO526289
EST:     GGCGTCGAGCGCGTCGCTGTCTCCCTCGACCTCTACAACCAGGGATCCGC                         GACTGCCTATGATGTGTCCATTAATGACGACTCTTGGCCAACAGAAGTGTT
genomic: GGCGTCGAGCGCGTCGCTGTCTCCCTCGACCTCTACAACCAGGGATCCGCgtgagcaccg ... cctattgcagGACTGCCTATGATGTGTCCATTAATGACGACTCTTGGCCAACAGAAGTGTT
EST: gi|18649161|gb|BM497980.1|BM497980
EST:     GGCGTCGAGCGCGTCGCCGTCTCCCTCGACCTCTACAACCAGGGATCCGC                         GACTGCCTATGATGTGTCCATTAATGACGACTCTTGGCCAACAGAAGTGTT
genomic: GGCGTCGAGCGCGTCGCTGTCTCCCTCGACCTCTACAACCAGGGATCCGCgtgagcaccg ... cctattgcagGACTGCCTATGATGTGTCCATTAATGACGACTCTTGGCCAACAGAAGTGTT
EST: gi|22819811|gb|BU499901.1|BU499901
EST:     GGCGTCGAGCGCGTCGCCGTCTCCCTCGACCTCTACAACCAGGGATCCGC                         GACTGCCTATGATGTGTCCATTAATGACGACTCTTGGCCAACAGAAGTGTT
genomic: GGCGTCGAGCGCGTCGCTGTCTCCCTCGACCTCTACAACCAGGGATCCGCgtgagcaccg ... cctattgcagGACTGCCTATGATGTGTCCATTAATGACGACTCTTGGCCAACAGAAGTGTT
EST: gi|18161892|gb|BM331731.1|BM331731
EST:     GGCGTCGAGCGCGTCGCTGTCTCCCTCGACCTCTACAACCAGGGATCCGC                         GACTGCCTATGATGTGTCCATTAATGACGACTCTTGGCCAACAGAAGTGTT
genomic: GGCGTCGAGCGCGTCGCTGTCTCCCTCGACCTCTACAACCAGGGATCCGCgtgagcaccg ... cctattgcagGACTGCCTATGATGTGTCCATTAATGACGACTCTTGGCCAACAGAAGTGTT
EST: gi|89249775|gb|DY621561.1|DY621561
EST:     GGCGTCGAGCGCGTCGCTGTCTCCCTCGACCTCTACAACCAGGGATCCGC                         GACTGCCTATGATGTGTCCATTAATGACGACTCTTGGCCAACAGAAGTGTT
genomic: GGCGTCGAGCGCGTCGCTGTCTCCCTCGACCTCTACAACCAGGGATCCGCgtgagcaccg ... cctattgcagGACTGCCTATGATGTGTCCATTAATGACGACTCTTGGCCAACAGAAGTGTT
EST: gi|16378806|gb|BI992621.1|BI992621
EST:     CAGGGATCCGC                         GACTGCCTATGATGTGTCCATTAATGACGACTCTTGGCCAACAGAAGTGTT
genomic: CAGGGATCCGCgtgagcaccg ... cctattgcagGACTGCCTATGATGTGTCCATTAATGACGACTCTTGGCCAACAGAAGTGTT
EST: gi|18168815|gb|BM338655.1|BM338655
EST:     CCCTCGACCTCTACAACCAGGGATCCGC                         GACTGCCTATGATGTGTCCATTAATGACGACTCTTGGCCAACAGAAGTGTT
genomic: CCCTCGACCTCTACAACCAGGGATCCGCgtgagcaccg ... cctattgcagGACTGCCTATGATGTGTCCATTAATGACGACTCTTGGCCAACAGAAGTGTT
EST: gi|18168659|gb|BM338499.1|BM338499
EST:     ACAACCAGGGATCCGC                         GACTGCCTATGATGTGTCCATTAATGACGACTCTTGGCCAACAGAAGTGTT
genomic: ACAACCAGGGATCCGCgtgagcaccg ... cctattgcagGACTGCCTATGATGTGTCCATTAATGACGACTCTTGGCCAACAGAAGTGTT
EST: gi|18649160|gb|BM497979.1|BM497979
EST:     GGCGTCGAGCGCGTCGCCGTCTCCCTCGACCTCTACAACCAGGGATCCGC                         GACTGCCTATGATGTGTCCATTAATGACGACTCTTGGCCAACAGAAGTGTT
genomic: GGCGTCGAGCGCGTCGCTGTCTCCCTCGACCTCTACAACCAGGGATCCGCgtgagcaccg ... cctattgcagGACTGCCTATGATGTGTCCATTAATGACGACTCTTGGCCAACAGAAGTGTT
EST: gi|18167604|gb|BM337444.1|BM337444
EST:     GGCGTCGAGCGCGTCGCTGTCTCCCTCGACCTCTACAACCAGGGATCCGC                         GACTGCCTATGATGTGTCCATTAATGACGACTCTTGGCCAACAGAAGTGTT
genomic: GGCGTCGAGCGCGTCGCTGTCTCCCTCGACCTCTACAACCAGGGATCCGCgtgagcaccg ... cctattgcagGACTGCCTATGATGTGTCCATTAATGACGACTCTTGGCCAACAGAAGTGTT
EST: gi|18174386|gb|BM349774.1|BM349774
EST:     AGCGCGTCGCTGTCTCCCTCGACCTCTACAACCAGGGATCCGC                         GACTGCCTATGATGTGTCCATTAATGACGACTCTTGGCCAACAGAAGTGTT
genomic: AGCGCGTCGCTGTCTCCCTCGACCTCTACAACCAGGGATCCGCgtgagcaccg ... cctattgcagGACTGCCTATGATGTGTCCATTAATGACGACTCTTGGCCAACAGAAGTGTT
EST: gi|18164000|gb|BM333839.1|BM333839
EST:     CCCTCGACCTCTACAACCAGGGATCCGC                         GACTGCCTATGATGTGTCCATTAATGACGACTCTTGGCCAACAGAAGTGTT
genomic: CCCTCGACCTCTACAACCAGGGATCCGCgtgagcaccg ... cctattgcagGACTGCCTATGATGTGTCCATTAATGACGACTCTTGGCCAACAGAAGTGTT
EST: gi|18174175|gb|BM349563.1|BM349563
EST:     GCGCGTCGCTGTCT-CCTCGAACCTCTACAACCAGGGATCCGC                         GACTGCCTATGATGTGTCCATTAATGACGACTCTTGGCCAACAGAAGTGTT
genomic: GCGCGTCGCTGTCTCCCTCG-ACCTCTACAACCAGGGATCCGCgtgagcaccg ... cctattgcagGACTGCCTATGATGTGTCCATTAATGACGACTCTTGGCCAACAGAAGTGTT
EST: gi|18173140|gb|BM348528.1|BM348528
EST:     GGCGTCGAGCGCGTCGCTGTCTCCCTCGACCTCTACAACCAGGGATCCGC                         GACTGCCTATGATGTGTCCATTAATGACGACTCTTGGCCAACAGAAGTGTT
genomic: GGCGTCGAGCGCGTCGCTGTCTCCCTCGACCTCTACAACCAGGGATCCGCgtgagcaccg ... cctattgcagGACTGCCTATGATGTGTCCATTAATGACGACTCTTGGCCAACAGAAGTGTT
EST: gi|18172051|gb|BM347439.1|BM347439
EST:     GGCGTCGAGCGCGTCGCTGTCTCCCTCGACCTCTACAACCAGGGATCCGC                         GACTGCCTATGATGTGTCCATTAATGACGACTCTTGGCCAACAGAAGTGTT
genomic: GGCGTCGAGCGCGTCGCTGTCTCCCTCGACCTCTACAACCAGGGATCCGCgtgagcaccg ... cctattgcagGACTGCCTATGATGTGTCCATTAATGACGACTCTTGGCCAACAGAAGTGTT
EST: gi|110524573|gb|EE028757.1|EE028757
EST:     ACCAGGGGATCCGC                         GACTGCCTATGATGTGTCCATTAATGACGACTCTTGGCCAACAGAAGTGT
genomic: ACCA-GGGATCCGCgtgagcaccg ... cctattgcagGACTGCCTATGATGTGTCCATTAATGACGACTCTTGGCCAACAGAAGTGT
EST: gi|37391749|gb|CF633118.1|CF633118
EST:     CCAGGGATCCGC                         GACTGCCTATGATGTGTCCATTAATGACGACTCTTGGCCAACAGAAGTGTA
genomic: CCAGGGATCCGCgtgagcaccg ... cctattgcagGACTGCCTATGATGTGTCCATTAATGACGACTCTTGGCCAACAGAAGTGTT
EST: gi|18163404|gb|BM333243.1|BM333243
EST:     GACCTCTACAACCAGGGATCCGC                         GACTGCATATGATGTGTCCATTAATGACGACTCTTGGCCAACAGAAGTGTT
genomic: GACCTCTACAACCAGGGATCCGCgtgagcaccg ... cctattgcagGACTGCCTATGATGTGTCCATTAATGACGACTCTTGGCCAACAGAAGTGTT
EST: gi|161590160|gb|EY960637.1|EY960637
EST:     GGCGTCGAGCGCGTCGCCGTCTCCCTCGACCTCTACAACCAGGGATCCGC                         GACTGCCTATGATGTGTCCATTAATGACGACTCTTGGCCAACA
genomic: GGCGTCGAGCGCGTCGCTGTCTCCCTCGACCTCTACAACCAGGGATCCGCgtgagcaccg ... cctattgcagGACTGCCTATGATGTGTCCATTAATGACGACTCTTGGCCAACA

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), 39 (downstream exon)
Score: 378

CGCCCTTCGTCGTCGCGCACAAGAAAATTTCGCTCTCCCGCCCCAAGCCGGGCGTCGAGCGCGTCGCTGTCTCCCTCGACCTCTACAACCAGGGATCCGCgtgagcaccg ... cctattgcagGACTGCCTATGATGTGTCCATTAATGACGACTCTTGGCCAACAGAAGTGTTTGAGCTTGTCACTGGAGAGAAATCGAAGACATTGGAAAGGCTTGACCC


Block sizes: 49 (upstream exon), 41 (downstream exon)
Score: 452

CGCCCTTCGTCGTCGCGCACAAGAAAATTTCGCTCTCCCGCCCCAAGCCGGGCGTCGAGCGCGTCGCTGTCTCCCTCGACCTCTACAACCAGGGATCCGCgtgagcaccg ... cctattgcagGACTGCCTATGATGTGTCCATTAATGACGACTCTTGGCCAACAGAAGTGTTTGAGCTTGTCACTGGAGAGAAATCGAAGACATTGGAAAGGCTTGACCC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 579

CGCCCTTCGTCGTCGCGCACAAGAAAATTTCGCTCTCCCGCCCCAAGCCGGGCGTCGAGCGCGTCGCTGTCTCCCTCGACCTCTACAACCAGGGATCCGCgtgagcaccg ... cctattgcagGACTGCCTATGATGTGTCCATTAATGACGACTCTTGGCCAACAGAAGTGTTTGAGCTTGTCACTGGAGAGAAATCGAAGACATTGGAAAGGCTTGACCC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 344

CGCCCTTCGTCGTCGCGCACAAGAAAATTTCGCTCTCCCGCCCCAAGCCGGGCGTCGAGCGCGTCGCTGTCTCCCTCGACCTCTACAACCAGGGATCCGCgtgagcaccg ... cctattgcagGACTGCCTATGATGTGTCCATTAATGACGACTCTTGGCCAACAGAAGTGTTTGAGCTTGTCACTGGAGAGAAATCGAAGACATTGGAAAGGCTTGACCC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caatcccatatgttctcatagcatctgcatggacttattgtaaaacctattgcagGACTGCCTATGATGTGTCCATTAATGACGACTCTTGGCCAACAGAAGTGTTTGAGCTTGTCACTGGAGAGAAATCGAAGACATTGGAAAGGCTTGACCC
                                  ttattgtaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgcatcatgtatatgtgctcccttccgtttcatatgacggcaaatcaatcccatatgttctcatagcatctgcatggacttattgtaaaacctattgcagGACTGCCTATGATGTGTCCATTAATGACGACTCTTGGCCAACAGAAGTGTTTGAGCTTGTCACTGGAGAGAAATCGAAGACATTGGAAAGGCTTGACCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - -catgtat
- - - - - - - -tgctccc
- - - - - - - - - - - - - - ttcatat
- - - - - - - - - - - - - - - - - - - - caaatcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcatgg