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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacacatgtaatttcgtggtgcaaaatcatgattgctatttggctttaaagagtcagttgagtaatcaaacgtttgttgattattcagTTTTACACAAAATTAGAAGAAAAACGCAAGGCTTTGGAAGAGGAGAAACTCCAAGCAGAGGCCAGAAAGAGG

Basic information

species Zea mays
transcript AC148167.6_FGT001
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC148167.6_FGT001 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os07g08790.1 (Oryza sativa), 3'ss of exon 4
gtacacatgtaatttcgtggtgcaaaatcatgattgctatttggctttaaagagtcagttgagtaatcaaacgtttgttgattattcagTTTTACACAAAATTAGAAGAAAAACGCAAGGCTTTGGAAGAGGAGAAACTCCAAGCAGAGGCCAGAAAGAGG
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gtacgtatttaatttcatcatactgtagagaaatggctttgtaagttaaaggggacagcattgtaat-aattattctagtaccgttcagTTTTACACAAAATTGGAAGAAAAACGCAAGGCCTTGGAAGAGGAGAAACTAGAAGCTGAGGCAAGAAAAAAG
















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|149082930|gb|EE172164.2|EE172164
EST:     CTGTTGCACCTACATTCGTCTGTGCTAATCGTGCTGAGAAGAGAGGAGAG                         TTTTACACAAAATTAGAAGAAAAACGCAAGGCTTTGGAAGAGGAGAAACTC
genomic: CTGTTGCACCTACATTCGTCTGTGCTAATCGTGCTGAGAAGAGAGGAGAGgtacacatgt ... gattattcagTTTTACACAAAATTAGAAGAAAAACGCAAGGCTTTGGAAGAGGAGAAACTC
EST: gi|149099639|gb|EE185684.2|EE185684
EST:     CTGTTGCACCTACATTCGTCTGTGCTAATCGTGCTGAGAAGAGAGGAGAG                         TTTTACACAAAATTAGAAGAAAAACGCAAGGCTTTGGAAGAGGAGAAACTC
genomic: CTGTTGCACCTACATTCGTCTGTGCTAATCGTGCTGAGAAGAGAGGAGAGgtacacatgt ... gattattcagTTTTACACAAAATTAGAAGAAAAACGCAAGGCTTTGGAAGAGGAGAAACTC
EST: gi|26457346|gb|CA828929.1|CA828929
EST:     CTGTTGCACCTACATTCGTCTGTGCTAATCGTGCTGAGAAGAGAGGAGAG                         TTTTACACAAAATTAGAAGAAAAACGCAAGGCTTTGGAAGAGGAGAAACTC
genomic: CTGTTGCACCTACATTCGTCTGTGCTAATCGTGCTGAGAAGAGAGGAGAGgtacacatgt ... gattattcagTTTTACACAAAATTAGAAGAAAAACGCAAGGCTTTGGAAGAGGAGAAACTC
EST: gi|149097420|gb|EE183276.2|EE183276
EST:     CTGTTGCACCTACATTCGTCTGTGCTAATCGTGCTGAGAAGAGAGGAGAG                         TTTTACACAAAATTAGAAGAAAAACGCAAGGCTTTGGAAGAGGAGAAACTC
genomic: CTGTTGCACCTACATTCGTCTGTGCTAATCGTGCTGAGAAGAGAGGAGAGgtacacatgt ... gattattcagTTTTACACAAAATTAGAAGAAAAACGCAAGGCTTTGGAAGAGGAGAAACTC
EST: gi|148968362|gb|EE019509.2|EE019509
EST:     CTGTTGCACCTACATTCGTCTGTGCTAATCGTGCTGAGAAGAGAGGAGAG                         TTTTACACAAAATTAGAAGAAAAACGCAAGGCTTTGGAAGAGGAGAAACTC
genomic: CTGTTGCACCTACATTCGTCTGTGCTAATCGTGCTGAGAAGAGAGGAGAGgtacacatgt ... gattattcagTTTTACACAAAATTAGAAGAAAAACGCAAGGCTTTGGAAGAGGAGAAACTC
EST: gi|148929700|gb|EC876422.2|EC876422
EST:     CTGTTGCACCTACATTCGTCTGTGCTAATCGTGCTGAGAAGAGAGGAGAG                         TTTTACACAAAATTAGAAGAAAAACGCAAGGCTTTGGGAGAGGAGAAACTC
genomic: CTGTTGCACCTACATTCGTCTGTGCTAATCGTGCTGAGAAGAGAGGAGAGgtacacatgt ... gattattcagTTTTACACAAAATTAGAAGAAAAACGCAAGGCTTTGGAAGAGGAGAAACTC
EST: gi|22472914|gb|BU037394.1|BU037394
EST:     CTGTTGCACCTACATTCGTCTGTGCTAATCGTGCTGAGAAGAGAGGAGAG                         TTTTACACAAAATTAGAAGAAAAACGCAAGGCTTTGGAAGAGGAGAAACTC
genomic: CTGTTGCACCTACATTCGTCTGTGCTAATCGTGCTGAGAAGAGAGGAGAGgtacacatgt ... gattattcagTTTTACACAAAATTAGAAGAAAAACGCAAGGCTTTGGAAGAGGAGAAACTC
EST: gi|211410393|gb|FL027532.1|FL027532
EST:     CTGTTGCACCTACATTCGTCTGTGCTAATCGTGCTGAGAAGAGAGGAGAG                         TTTTACACAAAATTAGAAGAAAAACGCAAGGCTTTGGAAGAGGAGAAACTC
genomic: CTGTTGCACCTACATTCGTCTGTGCTAATCGTGCTGAGAAGAGAGGAGAGgtacacatgt ... gattattcagTTTTACACAAAATTAGAAGAAAAACGCAAGGCTTTGGAAGAGGAGAAACTC
EST: gi|8367407|gb|BE050352.1|BE050352
EST:     CTGTTGCACCAACATTCGTCTGTGCTAATCGTGCTGAGAAGAGAGGAGAG                         TTTTACACAAAATTAGAAGAAAAGCGCAAGGCTTTGGAAGAGG
genomic: CTGTTGCACCTACATTCGTCTGTGCTAATCGTGCTGAGAAGAGAGGAGAGgtacacatgt ... gattattcagTTTTACACAAAATTAGAAGAAAAACGCAAGGCTTTGGAAGAGG
EST: gi|22545951|gb|BU098310.1|BU098310
EST:     CTGTTGCACCTACATTCGTCTGTGCTAATCGTGCTGAGAAGAGAGGAGAG                         TTTTACACAAAATTAGAAGAAAAACGCAAGGCTTTGGAAGAGGAGAAACTC
genomic: CTGTTGCACCTACATTCGTCTGTGCTAATCGTGCTGAGAAGAGAGGAGAGgtacacatgt ... gattattcagTTTTACACAAAATTAGAAGAAAAACGCAAGGCTTTGGAAGAGGAGAAACTC
EST: gi|22819470|gb|BU499560.1|BU499560
EST:     TGTTGCACCTACATTCGTCTGTGCTAATCGGTGCTGAGAAGAGAGGAGAG                         TTTTACACAAAATTAGAAGAAAAACGCAAGGCTTTGGAAGAGGAGAAACTC
genomic: TGTTGCACCTACATTCGTCTGTGCTAATC-GTGCTGAGAAGAGAGGAGAGgtacacatgt ... gattattcagTTTTACACAAAATTAGAAGAAAAACGCAAGGCTTTGGAAGAGGAGAAACTC
EST: gi|22472889|gb|BU037369.1|BU037369
EST:     CTGTTGCACCTACATTCGTCTGTGCTAATCGTGCTGAGAAGAGAGGAGAG                         TTTTACACAAAATTAGAAGAAAAACGCAAGGCTTTGGAAGAGGAGAAACTC
genomic: CTGTTGCACCTACATTCGTCTGTGCTAATCGTGCTGAGAAGAGAGGAGAGgtacacatgt ... gattattcagTTTTACACAAAATTAGAAGAAAAACGCAAGGCTTTGGAAGAGGAGAAACTC

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: 158

AACTGTAACTTCAGCAAGAGCTGGGAAAACTAAGAAGACAACTGTTGCTGTTGCACCTACATTCGTCTGTGCTAATCGTGCTGAGAAGAGAGGAGAGgtacacatgt ... gattattcagTTTTACACAAAATTAGAAGAAAAACGCAAGGCTTTGGAAGAGGAGAAACTCCAAGCAGAGGCCAGAAAGAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 84

AACTGTAACTTCAGCAAGAGCTGGGAAAACTAAGAAGACAACTGTTGCTGTTGCACCTACATTCGTCTGTGCTAATCGTGCTGAGAAGAGAGGAGAGgtacacatgt ... gattattcagTTTTACACAAAATTAGAAGAAAAACGCAAGGCTTTGGAAGAGGAGAAACTCCAAGCAGAGGCCAGAAAGAGG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 84

AACTGTAACTTCAGCAAGAGCTGGGAAAACTAAGAAGACAACTGTTGCTGTTGCACCTACATTCGTCTGTGCTAATCGTGCTGAGAAGAGAGGAGAGgtacacatgt ... gattattcagTTTTACACAAAATTAGAAGAAAAACGCAAGGCTTTGGAAGAGGAGAAACTCCAAGCAGAGGCCAGAAAGAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 220

AACTGTAACTTCAGCAAGAGCTGGGAAAACTAAGAAGACAACTGTTGCTGTTGCACCTACATTCGTCTGTGCTAATCGTGCTGAGAAGAGAGGAGAGgtacacatgt ... gattattcagTTTTACACAAAATTAGAAGAAAAACGCAAGGCTTTGGAAGAGGAGAAACTCCAAGCAGAGGCCAGAAAGAGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgctatttggctttaaagagtcagttgagtaatcaaacgtttgttgattattcagTTTTACACAAAATTAGAAGAAAAACGCAAGGCTTTGGAAGAGGAGAAACTCCAAGCAGAGGCCAGAAAGAGG
                                         tgttgat  putative branch site (score: 220)
                                           ttgattatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacacatgtaatttcgtggtgcaaaatcatgattgctatttggctttaaagagtcagttgagtaatcaaacgtttgttgattattcagTTTTACACAAAATTAGAAGAAAAACGCAAGGCTTTGGAAGAGGAGAAACTCCAAGCAGAGGCCAGAAAGAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG