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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcacttaattatacttatcctttgacttgctaaattcagtatgcactttttgtaaaattcgataatcatttctactgctatttaatagAAACGTGGGATGCAATCTACTGTGTATGTTGAATTGGCATCTGGAGTGACTCCCAGGGATTTGTATGAACACCTAAAGTCTACTTACGAG

Basic information

species Zea mays
transcript GRMZM2G038848_T02
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G038848_T02 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os03g42110.1 (Oryza sativa), 3'ss of exon 11
------------------gtaagcacttaattatacttatcctt-tgacttgctaaattcagtatgcactttttgtaaaattcgataa-tca----tttctactgc-tatttaatagAAACGTGGGATGCAATCTACTGTGTATGTTGAATTGGCATCTGGAGTGACTCCCAGGGATTTGTATGAACACCTAAAGTCTACTTACGAG
                   |    ||||| | || |    |  | |   |  ||   | | |||       | | || || | | ||| |||      ||  |||  ||||||| ||||||||||||||||||||||| |||  |||||| ||||| ||||||||||| |||  ||||||||| | || || |||||||| || |||
gtaagcacatttgcactcttgttgacttagtaattccaggctctgtagttccctctgtgctgtaccaggaatgtatagaagttgctaaatcaaatgactcatctgtatatttaacagAAACGTGGGATGCAATCTACTATGTTCGTTGAAATGGCACCTGGAGTGACTGCCAATGATTTGTATCAGCATCTCAAGTCTACATATGAG

upper sequence: GRMZM2G038848_T02 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os10g35170.1 (Oryza sativa), 3'ss of exon 11
gtaagcacttaattatacttatcctttgacttgctaaattcag--tatgcactttt----tgtaa-------------------------aattcgat--aatcatttctactgctatttaatagAAACGTGGGATGCAATCTACTGTGTATGTTGAATTGGCATCTGGAGTGACTCCCAGGGATTTGTATGAACACCTAAAGTCTACTTACGAG
||||||||||| ||   | | |   |||||||  ||| | |||  | |||| ||||    ||||                          | ||  ||  |||  ||  || |    || || |||||||||| |||||||||||  ||| ||||||| ||||| ||||||||||| || | ||||||||  | || || ||||||||||| |||
gtaagcacttactttctcatttttgttgacttaataactccaggttctgcagttttgtactgtattgaacgcacctggagtgtgtgcattagttaaatcaaattcttcatatttacgttgaacagAAACGTGGAATGCAATCTACCATGTTTGTTGAAATGGCACCTGGAGTGACTGCCGGTGATTTGTACCAGCATCTCAAGTCTACTTATGAG
















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|31354246|gb|CD438603.1|CD438603
EST:     CTGCTGAATCAAAAGTTACTATCAGCTTTACTCCACATTTGATGTGTATG                         AAACGTGGGATGCAATCTACTGTGTATGTTGAATTGGCATCTGGAGTGACT
genomic: CTGCTGAATCAAAAGTTACTATCAGCTTTACTCCACATTTGATGTGTATGgtaagcactt ... tatttaatagAAACGTGGGATGCAATCTACTGTGTATGTTGAATTGGCATCTGGAGTGACT
EST: gi|37397485|gb|CF636042.1|CF636042
EST:     TTTGATGTGTATG                         AAACGTGGGATGCAATCTACTGTGTATGTTGAATTGGCATCTGGAGTGACT
genomic: TTTGATGTGTATGgtaagcactt ... tatttaatagAAACGTGGGATGCAATCTACTGTGTATGTTGAATTGGCATCTGGAGTGACT
EST: gi|6448353|gb|AW181119.1|AW181119
EST:     CTGCTGAATCAAAAGTTACTATCAGCTTTACTCCACATTTGATGTGTATG                         AAACGTGGGATGCAATCTACTGTGTATGTTGAATTGGCATCTGGAGTGACT
genomic: CTGCTGAATCAAAAGTTACTATCAGCTTTACTCCACATTTGATGTGTATGgtaagcactt ... tatttaatagAAACGTGGGATGCAATCTACTGTGTATGTTGAATTGGCATCTGGAGTGACT
EST: gi|88747566|gb|DY531707.1|DY531707
EST:     CTGCTGAATCAAAAGTTACTATCAGCTTTACTCCACATTTGATGTGTATG                         AAACGTGGGATGCAATCTACTGTGTATGTTGAATTGGCATCTGGAGTGACT
genomic: CTGCTGAATCAAAAGTTACTATCAGCTTTACTCCACATTTGATGTGTATGgtaagcactt ... tatttaatagAAACGTGGGATGCAATCTACTGTGTATGTTGAATTGGCATCTGGAGTGACT
EST: gi|110202395|gb|EC884292.1|EC884292
EST:     CTGGGGAATCAAAAGTTACTTTCAGCTTTACTCCACATTTGATGTGTATG                         AAACGTGGGAGGCAATCTACTGTGTATGTTGAATTGGCATCTGGAGTGACT
genomic: CTGCTGAATCAAAAGTTACTATCAGCTTTACTCCACATTTGATGTGTATGgtaagcactt ... tatttaatagAAACGTGGGATGCAATCTACTGTGTATGTTGAATTGGCATCTGGAGTGACT
EST: gi|32930019|gb|CF034831.1|CF034831
EST:     AATCAAAAGTTACTATCAGCTTTACTCCACATTTGATGTGTATG                         AAACGTGGGATGCAATCTACTGTGTATGTTGAATTGGCATCTGGAGTGACT
genomic: AATCAAAAGTTACTATCAGCTTTACTCCACATTTGATGTGTATGgtaagcactt ... tatttaatagAAACGTGGGATGCAATCTACTGTGTATGTTGAATTGGCATCTGGAGTGACT
EST: gi|71762552|gb|DR960489.1|DR960489
EST:     CTGCTGAATCAAAAGTTACTATCAGCTTTACTCCACATTTGATGTGTATG                         AAACGTGGGATGCAATCTACTGTGTATGTTGAATTGGCATCTGGAGTGACT
genomic: CTGCTGAATCAAAAGTTACTATCAGCTTTACTCCACATTTGATGTGTATGgtaagcactt ... tatttaatagAAACGTGGGATGCAATCTACTGTGTATGTTGAATTGGCATCTGGAGTGACT
EST: gi|148958090|gb|EC904281.2|EC904281
EST:     CTGCTGAATCAAAAGTTACTATCAGCTTTACTCCACATTTGATGTGTATG                         AAACGTGGGATGCAATCTACTGTGTATGTTGAATTGGCATCTGGAGTGACT
genomic: CTGCTGAATCAAAAGTTACTATCAGCTTTACTCCACATTTGATGTGTATGgtaagcactt ... tatttaatagAAACGTGGGATGCAATCTACTGTGTATGTTGAATTGGCATCTGGAGTGACT
EST: gi|74234670|gb|DT642584.1|DT642584
EST:     CTGCTGAATCAAAAGTTACTATCAGCTTTACTCCACATTTGATGTGTATG                         AAACGTGGGATGCAATCTACTGTGTATGTTGAATTGGCATCTGGAGTGACT
genomic: CTGCTGAATCAAAAGTTACTATCAGCTTTACTCCACATTTGATGTGTATGgtaagcactt ... tatttaatagAAACGTGGGATGCAATCTACTGTGTATGTTGAATTGGCATCTGGAGTGACT
EST: gi|60394782|gb|DN227652.1|DN227652
EST:     CTGCTGAATCAAAAGTTACTATCAGCTTTACTCCACATTTGATGTGTATG                         AAACGTGGGATGCAATCTACTGTGTATGTTGAATTGGCATCTGGAGTGACT
genomic: CTGCTGAATCAAAAGTTACTATCAGCTTTACTCCACATTTGATGTGTATGgtaagcactt ... tatttaatagAAACGTGGGATGCAATCTACTGTGTATGTTGAATTGGCATCTGGAGTGACT
EST: gi|87155331|gb|DY400120.1|DY400120
EST:     CTGCTGAATCAAAAGTTACTATCAGCTTTACTCCACATTTGATGTGTATG                         AAACGTGGGATGCAATCTACTGTGTATGTTGAATTGGCATCTGGAGTGACT
genomic: CTGCTGAATCAAAAGTTACTATCAGCTTTACTCCACATTTGATGTGTATGgtaagcactt ... tatttaatagAAACGTGGGATGCAATCTACTGTGTATGTTGAATTGGCATCTGGAGTGACT
EST: gi|26558690|gb|CA830925.1|CA830925
EST:     CTGCTGAATCAAAAGTTACTATCAGCTTTACTCCACATTTGATGTGTATG                         AAACGTGGGATGCAATCTACTGTGTATGTTGAATTGGCATCTGGAGTGACT
genomic: CTGCTGAATCAAAAGTTACTATCAGCTTTACTCCACATTTGATGTGTATGgtaagcactt ... tatttaatagAAACGTGGGATGCAATCTACTGTGTATGTTGAATTGGCATCTGGAGTGACT
EST: gi|33093061|gb|CF053055.1|CF053055
EST:     CTGCTGAATCAAAAGTTACTATCAGCTTTACTCCACATTTGATGTGTATG                         AAACGTGGGATGCAATCTACTGTGTATGTTGAATTGGCATCTGGAGTGACT
genomic: CTGCTGAATCAAAAGTTACTATCAGCTTTACTCCACATTTGATGTGTATGgtaagcactt ... tatttaatagAAACGTGGGATGCAATCTACTGTGTATGTTGAATTGGCATCTGGAGTGACT
EST: gi|148942778|gb|EC887805.2|EC887805
EST:     TCAAAAGTTACTATCAGCTTTACTCCACATTGGATGTGTATG                         AAACGTGGGATGCAATCTACTGTGTATGTTGAATTGGCATCTGGAGTGACT
genomic: TCAAAAGTTACTATCAGCTTTACTCCACATTTGATGTGTATGgtaagcactt ... tatttaatagAAACGTGGGATGCAATCTACTGTGTATGTTGAATTGGCATCTGGAGTGACT
EST: gi|32931562|gb|CF036374.1|CF036374
EST:     CTGCTGAATCAAAAGTTACTATCAGCTTTACTCCACATTTGATGTGTATG                         AAACGTGGGATGCAATCTACTGTGTATGTTGAATTGGCATCTGGAGTGACT
genomic: CTGCTGAATCAAAAGTTACTATCAGCTTTACTCCACATTTGATGTGTATGgtaagcactt ... tatttaatagAAACGTGGGATGCAATCTACTGTGTATGTTGAATTGGCATCTGGAGTGACT
EST: gi|40337039|gb|CK371109.1|CK371109
EST:     TTTGATGTGTATG                         AAACGTGGGATGCAATCTACTGTGTATGTTGAATTGGCATCTGGAGTGACT
genomic: TTTGATGTGTATGgtaagcactt ... tatttaatagAAACGTGGGATGCAATCTACTGTGTATGTTGAATTGGCATCTGGAGTGACT
EST: gi|78080159|gb|DV508571.1|DV508571
EST:     CTGCTGAATCAAAAGTTACTATCAGCTTTACTCCACATTTGATGTGTATG                         AAACGTGGGATGCAATCTACTGTGTATGTTGAATTGGCATCTGGAGTGACT
genomic: CTGCTGAATCAAAAGTTACTATCAGCTTTACTCCACATTTGATGTGTATGgtaagcactt ... tatttaatagAAACGTGGGATGCAATCTACTGTGTATGTTGAATTGGCATCTGGAGTGACT
EST: gi|22473066|gb|BU037546.1|BU037546
EST:     CTGCTGAATCAAAAGTTACTATCAGCTTTACTCCACATTTGATGTGTATG                         AAACGTGGGATGCAATCTACTGTGTATGTTGAATTGGCATCTGGAGTGACT
genomic: CTGCTGAATCAAAAGTTACTATCAGCTTTACTCCACATTTGATGTGTATGgtaagcactt ... tatttaatagAAACGTGGGATGCAATCTACTGTGTATGTTGAATTGGCATCTGGAGTGACT
EST: gi|148943027|gb|EC888077.2|EC888077
EST:     CTGGTGAATCAAAAGTTACTATCAGCTTTACTCCACATTTGATGTGTATG                         AAACGTGGGAGGCAATCTCCTGTGTATGTTGAATTGGCATCTGGAGTGACT
genomic: CTGCTGAATCAAAAGTTACTATCAGCTTTACTCCACATTTGATGTGTATGgtaagcactt ... tatttaatagAAACGTGGGATGCAATCTACTGTGTATGTTGAATTGGCATCTGGAGTGACT
EST: gi|67010559|gb|CO439308.1|CO439308
EST:     CTGCTGAATCAAAAGTTACTATCAGCTTTACTCCACATTTGATGTGTATG                         AAACGTGGGATGCAATCTACTGTGTATGTTGAATTGGCATCTGGAGTGACT
genomic: CTGCTGAATCAAAAGTTACTATCAGCTTTACTCCACATTTGATGTGTATGgtaagcactt ... tatttaatagAAACGTGGGATGCAATCTACTGTGTATGTTGAATTGGCATCTGGAGTGACT

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), 44 (downstream exon)
Score: 118

TGCCTGAGATTGAGCAAGGACTTACAGATGCTGCTGAATCAAAAGTTACTATCAGCTTTACTCCACATTTGATGTGTATGgtaagcactt ... tatttaatagAAACGTGGGATGCAATCTACTGTGTATGTTGAATTGGCATCTGGAGTGACTCCCAGGGATTTGTATGAACACCTAAAGTCTACTTACGAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 110

TGCCTGAGATTGAGCAAGGACTTACAGATGCTGCTGAATCAAAAGTTACTATCAGCTTTACTCCACATTTGATGTGTATGgtaagcactt ... tatttaatagAAACGTGGGATGCAATCTACTGTGTATGTTGAATTGGCATCTGGAGTGACTCCCAGGGATTTGTATGAACACCTAAAGTCTACTTACGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 124

TGCCTGAGATTGAGCAAGGACTTACAGATGCTGCTGAATCAAAAGTTACTATCAGCTTTACTCCACATTTGATGTGTATGgtaagcactt ... tatttaatagAAACGTGGGATGCAATCTACTGTGTATGTTGAATTGGCATCTGGAGTGACTCCCAGGGATTTGTATGAACACCTAAAGTCTACTTACGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 99

TGCCTGAGATTGAGCAAGGACTTACAGATGCTGCTGAATCAAAAGTTACTATCAGCTTTACTCCACATTTGATGTGTATGgtaagcactt ... tatttaatagAAACGTGGGATGCAATCTACTGTGTATGTTGAATTGGCATCTGGAGTGACTCCCAGGGATTTGTATGAACACCTAAAGTCTACTTACGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attcagtatgcactttttgtaaaattcgataatcatttctactgctatttaatagAAACGTGGGATGCAATCTACTGTGTATGTTGAATTGGCATCTGGAGTGACTCCCAGGGATTTGTATGAACACCTAAAGTCTACTTACGAG
           actttttgtaaaatt  TA-rich tract