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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagaactcaaaatctttcatttgtttagtaactggtggacaaaaatatgaggtttacacagtagtgaaactgaatagttacaacactggatttttactttgagtttcatattgcagGAGTAGTTATTTATGGTGGACCTGTTGCACATGACAAGTTGAAAGTACCAAAGGTAGACTCATTTCGTCATGAGTATAGCTCAATGGCATGCACAGTCGA

Basic information

species Zea mays
transcript GRMZM2G028535_T02
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G028535_T02 (Zea mays), 3'ss of exon 15
lower sequence: LOC_Os01g62900.1 (Oryza sativa), 3'ss of exon 15
gtcagaactcaaaatctttcatttgtttagtaactggtggacaaaaatatgaggtttacacagtagtgaaactgaatagttacaacactggatttttactttgagtttcatattgcagGAGTAGTTATTTATGGTGGACCTGTTGCACATGACAAGTTGAAAGTACCAAAGGTAGACTCATTTCGTCATGAGTATAGCTCAATGGCATGCACAGTCGA
                   || |   |    || || |   ||| |  |     | | || |  ||  |||  | ||    | | ||||      ||    |   | |||| ||||||| |||||||| ||||| || ||||||||||||||||  |||||| ||||||||||||| ||||||| ||||||||||| |||||||||||||||  ||||
------------------gcagtcaatccaaaattgctttgcaacacgagttcttgtgcaaatcagcaaaaggggatcagaagagcactaatggattttaattgatgtcatgttgcagGGGTAGTTATCTATGGCGGGCCTGTTGCACATGACACTTTGAAACTACCAAAGGTAGATTCATTTCATCATGAGTATAACTCAATGGCATGCACCCTCGA
















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|32931318|gb|CF036130.1|CF036130
EST:     TAACAAGAGTGAGGGACTTGATGATCTATTAGTGGAACTTGAAAAGGAAG                         GAGTAGTTATTTATGGTGGACCTGTTGCACATGACAAGTTGAAAGT
genomic: TAACAAGAGTGAGGGACTTGATGATCTATTAGTGGAACTTGAAAAGGAAGgtcagaactc ... catattgcagGAGTAGTTATTTATGGTGGACCTGTTGCACATGACAAGTTGAAAGT
EST: gi|33094388|gb|CF054382.1|CF054382
EST:     TAACAAGAGTGAGGGACTTGATGATCTATTAGTGGAACTTGAAAAGGAAG                         GAGTAGTTATTTATGGTGGACCTGTTGCACATGACAAGCTGAAAGT
genomic: TAACAAGAGTGAGGGACTTGATGATCTATTAGTGGAACTTGAAAAGGAAGgtcagaactc ... catattgcagGAGTAGTTATTTATGGTGGACCTGTTGCACATGACAAGTTGAAAGT
EST: gi|33091121|gb|CF051115.1|CF051115
EST:     TAACAAGAGTGAGGGACTTGATGATCTATTAGTGGAACTTGAAAAGGAAG                         GAGTAGTTATTTATGGTGGACCTGTTGCACGTGACAAGTTGAAAGTA
genomic: TAACAAGAGTGAGGGACTTGATGATCTATTAGTGGAACTTGAAAAGGAAGgtcagaactc ... catattgcagGAGTAGTTATTTATGGTGGACCTGTTGCACATGACAAGTTGAAAGTA
EST: gi|32931519|gb|CF036331.1|CF036331
EST:     TAACAAGAGTGAGGGACTTGATGATCTATTAGTGGAACTTGAAAAGGAAG                         GAGTAGTTATTTATGGTGGACCTGTTGCACATGACAAGTTGAAAGTA
genomic: TAACAAGAGTGAGGGACTTGATGATCTATTAGTGGAACTTGAAAAGGAAGgtcagaactc ... catattgcagGAGTAGTTATTTATGGTGGACCTGTTGCACATGACAAGTTGAAAGTA
EST: gi|61118748|gb|DN559709.1|DN559709
EST:     TAACAAGAGTGAGGGACTTGATGATCTATTAGTGGAACTTGAAAAGGAAG                         GAGTAGTTATTTATGGTGGACCTGTTGCACATGACAAACTGAAAGTACCAA
genomic: TAACAAGAGTGAGGGACTTGATGATCTATTAGTGGAACTTGAAAAGGAAGgtcagaactc ... catattgcagGAGTAGTTATTTATGGTGGACCTGTTGCACATGACAAGTTGAAAGTACCAA
EST: gi|24934245|gb|CA452463.1|CA452463
EST:     TAACAAGAGTGAGGGACTTGATGATCTATTAGTGGAACTTGAAAAGGAAG                         GAGTAGTTATTTATGGTGGACCTGTTGCACATGACAAGTTGAAAGT
genomic: TAACAAGAGTGAGGGACTTGATGATCTATTAGTGGAACTTGAAAAGGAAGgtcagaactc ... catattgcagGAGTAGTTATTTATGGTGGACCTGTTGCACATGACAAGTTGAAAGT
EST: gi|60344250|gb|DN211223.1|DN211223
EST:     ACAAGAGTGAGGGACTTGATGATCTATTAGTGGAACTTGAAAAGGAAG                         GAGTAGTTATTTATGGTGGACCTGTTGCACATGACAAGTTGAAAGTACCAA
genomic: ACAAGAGTGAGGGACTTGATGATCTATTAGTGGAACTTGAAAAGGAAGgtcagaactc ... catattgcagGAGTAGTTATTTATGGTGGACCTGTTGCACATGACAAGTTGAAAGTACCAA
EST: gi|60355192|gb|DN222165.1|DN222165
EST:     ACTTGATGATCTATTAGTGGAACTTGAAAAGGAAG                         GAGTAGTTATTTATGGTGGACCTGTTGCACATGACAAGTTGAAAGTACCAA
genomic: ACTTGATGATCTATTAGTGGAACTTGAAAAGGAAGgtcagaactc ... catattgcagGAGTAGTTATTTATGGTGGACCTGTTGCACATGACAAGTTGAAAGTACCAA
EST: gi|32932079|gb|CF036891.1|CF036891
EST:     TAACAAGAGTGAGGGACTTGATGATCTATTAGTGGAACTTGAAAAGGAAG                         GAGTAGTTATTTATGGTGGACCTGTTGCACATGACAAGTTGAAAGTACC
genomic: TAACAAGAGTGAGGGACTTGATGATCTATTAGTGGAACTTGAAAAGGAAGgtcagaactc ... catattgcagGAGTAGTTATTTATGGTGGACCTGTTGCACATGACAAGTTGAAAGTACC

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), 46 (downstream exon)
Score: 92

GAAACACTACTTGTTCATAAAGATCTTAACAAGAGTGAGGGACTTGATGATCTATTAGTGGAACTTGAAAAGGAAGgtcagaactc ... catattgcagGAGTAGTTATTTATGGTGGACCTGTTGCACATGACAAGTTGAAAGTACCAAAGGTAGACTCATTTCGTCATGAGTATAGCTCAATGGCATGCACAGTCGA


Block sizes: 46 (upstream exon), 43 (downstream exon)
Score: 8

GAAACACTACTTGTTCATAAAGATCTTAACAAGAGTGAGGGACTTGATGATCTATTAGTGGAACTTGAAAAGGAAGgtcagaactc ... catattgcagGAGTAGTTATTTATGGTGGACCTGTTGCACATGACAAGTTGAAAGTACCAAAGGTAGACTCATTTCGTCATGAGTATAGCTCAATGGCATGCACAGTCGA


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 4

GAAACACTACTTGTTCATAAAGATCTTAACAAGAGTGAGGGACTTGATGATCTATTAGTGGAACTTGAAAAGGAAGgtcagaactc ... catattgcagGAGTAGTTATTTATGGTGGACCTGTTGCACATGACAAGTTGAAAGTACCAAAGGTAGACTCATTTCGTCATGAGTATAGCTCAATGGCATGCACAGTCGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 294

GAAACACTACTTGTTCATAAAGATCTTAACAAGAGTGAGGGACTTGATGATCTATTAGTGGAACTTGAAAAGGAAGgtcagaactc ... catattgcagGAGTAGTTATTTATGGTGGACCTGTTGCACATGACAAGTTGAAAGTACCAAAGGTAGACTCATTTCGTCATGAGTATAGCTCAATGGCATGCACAGTCGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagtgaaactgaatagttacaacactggatttttactttgagtttcatattgcagGAGTAGTTATTTATGGTGGACCTGTTGCACATGACAAGTTGAAAGTACCAAAGGTAGACTCATTTCGTCATGAGTATAGCTCAATGGCATGCACAGTCGA
                            atttttacttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagaactcaaaatctttcatttgtttagtaactggtggacaaaaatatgaggtttacacagtagtgaaactgaatagttacaacactggatttttactttgagtttcatattgcagGAGTAGTTATTTATGGTGGACCTGTTGCACATGACAAGTTGAAAGTACCAAAGGTAGACTCATTTCGTCATGAGTATAGCTCAATGGCATGCACAGTCGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA