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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cgtgctatgtttccgcttggccaaaagaagggatacttggtgcatagatgtgcaggactaacattattggaatcggcataatgactcccacatatttcagGTTAAGGCCCTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAACGTTCAG

Basic information

species Zea mays
transcript GRMZM2G112793_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G112793_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g07150.1 (Oryza sativa), 3'ss of exon 1
cgtgctatgtttccgcttggccaaaagaagggatacttggt--gcatagatgt--gcaggacta--------acattattggaatcggcataatgact------cccacatatttcagGTTAAGGCCCTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAACGTTCAG
                 || ||||||  ||| | | ||| |  ||||| ||||   ||  |||         | |||  |||||||  | |     ||      ||| || ||| |||||||| || ||||||||||||||||||||||||||||||||||||||||| ||||||
-----------------tgaccaaaaataggaacatttgatgggcataaatgtctacacaactggtgttcttatattcctggaatctacgtgtgttctaatggaccctca-attgcagGTTAAAGCACTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAATGTTCAG
















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|22818811|gb|BU498901.1|BU498901
EST:     ACGCGCAGATCGAGCAGCTGATGCAGTGCCGCCCGCTCGCCGAGCAGGAG                         GTTAAGGCCCTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAAC
genomic: ACGCGCAGATCGAGCAGCTGATGCAGTGCCGCCCGCTCGCCGAGCAGGAGgtgagatcca ... catatttcagGTTAAGGCCCTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAAC
EST: gi|22490124|gb|BU050047.1|BU050047
EST:     ACGCGCAGATCGAGCAGCTGATGCAGTGCCGCCCGCTCGCCGAGCAGGAG                         GTTAAGGCCCTGTGCGAGAAGGCCAAGGAGTTATTGATGGAGGAAAGCAAC
genomic: ACGCGCAGATCGAGCAGCTGATGCAGTGCCGCCCGCTCGCCGAGCAGGAGgtgagatcca ... catatttcagGTTAAGGCCCTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAAC
EST: gi|211046221|gb|FL204514.1|FL204514
EST:     ACGCGCAGATCGAGCAGCTGATGCAGTGCCGCCCGCTCGCCGAGCAGGAG                         GTTAAGGCCCTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAAC
genomic: ACGCGCAGATCGAGCAGCTGATGCAGTGCCGCCCGCTCGCCGAGCAGGAGgtgagatcca ... catatttcagGTTAAGGCCCTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAAC
EST: gi|211043271|gb|FL204511.1|FL204511
EST:     ACGCGCAGATCGAGCAGCTGATGCAGTGCCGCCCGCTCGCCGAGCAGGAG                         GTTAAGGCCCTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAAC
genomic: ACGCGCAGATCGAGCAGCTGATGCAGTGCCGCCCGCTCGCCGAGCAGGAGgtgagatcca ... catatttcagGTTAAGGCCCTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAAC
EST: gi|211046223|gb|FL204516.1|FL204516
EST:     ACGCGCAGATCGAGCAGCTGATGCAGTGCCGCCCGCTCGCCGAGCAGGAG                         GTTAAGGCCCTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAAC
genomic: ACGCGCAGATCGAGCAGCTGATGCAGTGCCGCCCGCTCGCCGAGCAGGAGgtgagatcca ... catatttcagGTTAAGGCCCTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAAC
EST: gi|211046224|gb|FL204517.1|FL204517
EST:     ACGCGCAGATCGAGCAGCTGATGCAGTGCCGCCCGCTCGCCGAGCAGGAG                         GTTAAGGCCCTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAAC
genomic: ACGCGCAGATCGAGCAGCTGATGCAGTGCCGCCCGCTCGCCGAGCAGGAGgtgagatcca ... catatttcagGTTAAGGCCCTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAAC
EST: gi|211043272|gb|FL204512.1|FL204512
EST:     ACGCGCAGATCGAGCAGCTGATGCAGTGCCGCCCGCTCGCCGAGCAGGAG                         GTTAAGGCCCTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAAC
genomic: ACGCGCAGATCGAGCAGCTGATGCAGTGCCGCCCGCTCGCCGAGCAGGAGgtgagatcca ... catatttcagGTTAAGGCCCTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAAC
EST: gi|78118757|gb|DV537141.1|DV537141
EST:     ACGCGCAGATCGAGCAGCTGATGCAGTGCCGCCCGCTCGCCGAGCAGGAG                         GTTAAGGCCCTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAAC
genomic: ACGCGCAGATCGAGCAGCTGATGCAGTGCCGCCCGCTCGCCGAGCAGGAGgtgagatcca ... catatttcagGTTAAGGCCCTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAAC
EST: gi|26559743|gb|CA831978.1|CA831978
EST:     ACGCGCAGATCGAGCAGCTGATGCAGTGCCGCCCGCTCGCCGAGCAGGAG                         GTTAAGGCCCTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAAC
genomic: ACGCGCAGATCGAGCAGCTGATGCAGTGCCGCCCGCTCGCCGAGCAGGAGgtgagatcca ... catatttcagGTTAAGGCCCTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAAC
EST: gi|211043270|gb|FL204510.1|FL204510
EST:     ACGCGCAGATCGAGCAGCTGATGCAGTGCCGCCCGCTCGCCGAGCAGGAG                         GTTAAGGCCCTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAAC
genomic: ACGCGCAGATCGAGCAGCTGATGCAGTGCCGCCCGCTCGCCGAGCAGGAGgtgagatcca ... catatttcagGTTAAGGCCCTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAAC
EST: gi|211046225|gb|FL204518.1|FL204518
EST:     ACGCGCAGATCGAGCAGCTGATGCAGTGCCGCCCGCTCGCCGAGCAGGAG                         GTTAAGGCCCTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAAC
genomic: ACGCGCAGATCGAGCAGCTGATGCAGTGCCGCCCGCTCGCCGAGCAGGAGgtgagatcca ... catatttcagGTTAAGGCCCTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAAC
EST: gi|18655213|gb|BM500018.1|BM500018
EST:     ACGCGCAGATCGAGCAGCTGATGCAGTGCCGCCCGCTCGCCGAGCAGGAG                         GTTAAGGCCCTGTGCGAGAAGGCCAAGGAGATATTGATGGCAGGAAAGCAA
genomic: ACGCGCAGATCGAGCAGCTGATGCAGTGCCGCCCGCTCGCCGAGCAGGAGgtgagatcca ... catatttcagGTTAAGGCCCTGTGCGAGAAGGCCAAGGAGATATTGATGG-AGGAAAGCAA
EST: gi|6021718|gb|AW066646.1|AW066646
EST:     ACGCGCAGATCGAGCAGCTGATGCAGTGCCGCCCGCTCGCCGAGCAGGAG                         GTTAAGGCCCTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAAC
genomic: ACGCGCAGATCGAGCAGCTGATGCAGTGCCGCCCGCTCGCCGAGCAGGAGgtgagatcca ... catatttcagGTTAAGGCCCTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAAC
EST: gi|31360213|gb|CD444570.1|CD444570
EST:     ACGCGCAGAGGGAGCAGCTGATGCAGTGCCGCCCGCTCGCCGAGCAGGAG                         GTTAAGGCCCTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAAC
genomic: ACGCGCAGATCGAGCAGCTGATGCAGTGCCGCCCGCTCGCCGAGCAGGAGgtgagatcca ... catatttcagGTTAAGGCCCTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAAC
EST: gi|211043273|gb|FL204513.1|FL204513
EST:     ACGCGCAGATCGAGCAGCTGATGCGGTGCCGCCCGCTCGCCGAGCAGGAC                         GTTAAGGCCCTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAAC
genomic: ACGCGCAGATCGAGCAGCTGATGCAGTGCCGCCCGCTCGCCGAGCAGGAGgtgagatcca ... catatttcagGTTAAGGCCCTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAAC
EST: gi|26557712|gb|CA829947.1|CA829947
EST:     ACGCGCAGATCGAGCAGCTGATGCAGTGCCGCCCGCTCGCCGAGCAGGAG                         GTTAAGGCCCTGTGTCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAA
genomic: ACGCGCAGATCGAGCAGCTGATGCAGTGCCGCCCGCTCGCCGAGCAGGAGgtgagatcca ... catatttcagGTTAAGGCCCTGTG-CGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAA
EST: gi|87153205|gb|DY397994.1|DY397994
EST:     ACGCGCAGATCGAGCAGCTGATGCAGTGCCGCCCGCTCGCCGAGCAGGAG                         GTTAAGGCCCTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAAC
genomic: ACGCGCAGATCGAGCAGCTGATGCAGTGCCGCCCGCTCGCCGAGCAGGAGgtgagatcca ... catatttcagGTTAAGGCCCTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAAC
EST: gi|22541924|gb|BU092362.1|BU092362
EST:     CGCGCAGATCGAGCAGCTGATGCAGTGCCGCCCGCTCGCCGAGCAGGAG                         GTTAAGGCCCTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAAC
genomic: CGCGCAGATCGAGCAGCTGATGCAGTGCCGCCCGCTCGCCGAGCAGGAGgtgagatcca ... catatttcagGTTAAGGCCCTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAAC
EST: gi|211046226|gb|FL204519.1|FL204519
EST:     ACGCGCAGATCGAGCAGCTGATGCAGTGCCGCCCGCTCGCCGAGCAGGAG                         GTTAAGGCCCTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAAC
genomic: ACGCGCAGATCGAGCAGCTGATGCAGTGCCGCCCGCTCGCCGAGCAGGAGgtgagatcca ... catatttcagGTTAAGGCCCTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAAC

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: 48 (upstream exon), 49 (downstream exon)
Score: 218

CCGCGGTATGGATCCCATGAACGTAGACAACGGCGGCTGCGGCGGCCTTGACGCGCAGATCGAGCAGCTGATGCAGTGCCGCCCGCTCGCCGAGCAGGAGgtgagatcca ... catatttcagGTTAAGGCCCTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAACGTTCAG


Block sizes: 49 (upstream exon), 41 (downstream exon)
Score: 141

CCGCGGTATGGATCCCATGAACGTAGACAACGGCGGCTGCGGCGGCCTTGACGCGCAGATCGAGCAGCTGATGCAGTGCCGCCCGCTCGCCGAGCAGGAGgtgagatcca ... catatttcagGTTAAGGCCCTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAACGTTCAG


Block sizes: 49 (upstream exon), 41 (downstream exon)
Score: 156

CCGCGGTATGGATCCCATGAACGTAGACAACGGCGGCTGCGGCGGCCTTGACGCGCAGATCGAGCAGCTGATGCAGTGCCGCCCGCTCGCCGAGCAGGAGgtgagatcca ... catatttcagGTTAAGGCCCTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAACGTTCAG


Block sizes: 47 (upstream exon), 41 (downstream exon)
Score: 136

CCGCGGTATGGATCCCATGAACGTAGACAACGGCGGCTGCGGCGGCCTTGACGCGCAGATCGAGCAGCTGATGCAGTGCCGCCCGCTCGCCGAGCAGGAGgtgagatcca ... catatttcagGTTAAGGCCCTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAACGTTCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agatgtgcaggactaacattattggaatcggcataatgactcccacatatttcagGTTAAGGCCCTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAACGTTCAG
          gactaac  putative branch site (score: 136)
                                       ctcccac  putative PPT
             taacattatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cgtgctatgtttccgcttggccaaaagaagggatacttggtgcatagatgtgcaggactaacattattggaatcggcataatgactcccacatatttcagGTTAAGGCCCTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAACGTTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - atgtttc
- - - - - - - - - - - aaaagaa
- - - - - - - - - - - - - - - - - - - -gtgcata
- - - - - - - - - - - - - - - - - - - - - - - - -gtgcagg