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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctggcataattttctgcttgctaacacaaatataatgattggagtgtatgcgccattattatgaacaaactaactaatacaaatctggccgtagtgcagATATGCAAGTTCTTCCTACAGCAGCGATGTCGATTTGGTAGTAACTGCCGCATGTCTCATG

Basic information

species Zea mays
transcript GRMZM2G017923_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G017923_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g55000.1 (Oryza sativa), 3'ss of exon 2
----tctggcataattttctgcttgctaacacaaatataatgattggagtgtatgcgccattattatgaacaaactaactaatacaaatctggccgtagtgcagATATGCAAGTTCTTCCTACAGCAGCGATGTCGATTTGGTAGTAACTGCCGCATGTCTCATG
    ||   |||| ||||||| | | |||    ||| |||||    ||   || |   |||| |||  |||||| ||||||||   |||||| || |||||||||| |||||||| || || ||||| |||||||| |||||||||||||||||| |||| ||||
accatcaaccata-ttttctgttggttaatg-gaatgtaatgtccagaacataaggttcattgttaccaacaaattaactaatc--aatctgcccatagtgcagATGTGCAAGTTTTTTCTCCAGCAACGATGTCGGTTTGGTAGTAACTGCCGCTTGTCCCATG

upper sequence: GRMZM2G017923_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA08G43320.1 (Glycine max), 3'ss of exon 2
-tctggcataattttctgcttgctaacacaaatat--aatgattggagtgtatgcgccattattatgaacaaactaactaatacaaatctggccgtagtgcagATATGCAAGTTCTTCCTACAGCAGCGATGTCGATTTGGTAGTAACTGCCGCATGTCTCATG
 | |  | |  || | | ||  | ||      |    ||| |||  |    ||       | ||    |  |    |||||||| |      ||  ||||||||| |||||||||||  |||| || ||||||||||||||||||||||| ||| | || ||||
ctttaacgttgttat-tcctcccaaattttggttccaaattattcaataaaatcaattgct-tttcatatcattgtactaatactagaaca-ccaaagtgcagATGTGCAAGTTCTTTTTACAACAACGATGTCGATTTGGTAGTAACTGTCGCCTATCACATG

upper sequence: GRMZM2G017923_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA18G10210.1 (Glycine max), 3'ss of exon 2
-tctggcataattttctgcttgctaacacaaatat--aatgattggagtgtatgcgccattattatgaacaaactaactaatacaaatctggccgtagtgcagATATGCAAGTTCTTCCTACAGCAGCGATGTCGATTTGGTAGTAACTGCCGCATGTCTCATG
   |  |||  || | | ||  | ||      |    ||| |||  |    ||       | || | | ||   || ||||||| |    | ||  ||||||||| |||||||||||  |||| || ||||||||||||||||||||||| ||| | || ||||
ccttaacattgttat-tcctcccaaattttggttccaaattattcaatcaaatcaattgcttttcttatcattgta-ctaatactagaacg-ccaaagtgcagATGTGCAAGTTCTTTTTACAACAACGATGTCGATTTGGTAGTAACTGTCGCCTATCACATG

upper sequence: GRMZM2G017923_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv04s0008g07000.t01 (Vitis vinifera), 3'ss of exon 2
tctggcataattt----tctgcttgctaacacaaatataatgattggagtgtatgcgccattattatgaacaaactaactaatacaaatctggccgtagtgcagATATGCAAGTTCTTCCTACAGCAGCGATGTCGATTTGGTAGTAACTGCCGCATGTCTCATG
  |    | |||     | | |||| |       ||| ||  ||  ||||      |   |  | |   || |||| |||||| | |  |   || |||||||||||||||||||||| |||||||| ||||| |||||||| |  ||||||||| | || ||||
-ttaatgtcattggaaattttcttgttctagagcatagaaacataagagtcctctggttttggtcac--accaacttactaatgctagacca-ccctagtgcagATATGCAAGTTCTTTCTACAGCAACGATGCCGATTTGGCACCAACTGCCGCTTATCACATG

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|71775037|gb|DR972915.1|DR972915
EST:     CAGGCGATGCAAGGATCTCATTTCTGACACCTACATCTGAAAATATGTCG                         ATATGCAAGTTCTTCCTACAGCAGCGATGTCGATTTGGTGGTAACTGCCGC
genomic: CAGGCGATGCAAGGATCTCATTTCTGACACCTACATCTGAAAATATGTCGgtgagttatc ... cgtagtgcagATATGCAAGTTCTTCCTACAGCAGCGATGTCGATTTGGTAGTAACTGCCGC
EST: gi|78088366|gb|DV516759.1|DV516759
EST:     CAGGCGATGCAAGGATCTCATTTCTGACACCTACATCTGAAAATATGTCG                         ATATGCAAGTTCTTCCTACAGCAGCGATGTCGATTTGGTAGTAACTGCCGC
genomic: CAGGCGATGCAAGGATCTCATTTCTGACACCTACATCTGAAAATATGTCGgtgagttatc ... cgtagtgcagATATGCAAGTTCTTCCTACAGCAGCGATGTCGATTTGGTAGTAACTGCCGC
EST: gi|149081356|gb|EE170470.2|EE170470
EST:     CAGGCGATGCAAGGATCTCATTTCTGACACCTACATCTGAAAATATGTCG                         ATATGCAAGTTCTTCCTACAGCAGCGATGTCGATTTGGTAGTAACTGCCGC
genomic: CAGGCGATGCAAGGATCTCATTTCTGACACCTACATCTGAAAATATGTCGgtgagttatc ... cgtagtgcagATATGCAAGTTCTTCCTACAGCAGCGATGTCGATTTGGTAGTAACTGCCGC
EST: gi|149073984|gb|EE162314.2|EE162314
EST:     CAGGCGATGCAAGGATCTCATTTCTGACACCTACATCTGAAAATATGTCG                         ATATGCAAGTTCTTCCTACAGCAGCGATGTCGATTTGGTAGTAACTGCCGC
genomic: CAGGCGATGCAAGGATCTCATTTCTGACACCTACATCTGAAAATATGTCGgtgagttatc ... cgtagtgcagATATGCAAGTTCTTCCTACAGCAGCGATGTCGATTTGGTAGTAACTGCCGC
EST: gi|74245804|gb|DT653718.1|DT653718
EST:     CAGGCGATGCAAGGATCTCATTTCTGACACCTACATCTGAAAATATGTCG                         ATATGCAAGTTCTTCCTACAGCAGCGATGTCGATTTGGTAGTAACTGCCGC
genomic: CAGGCGATGCAAGGATCTCATTTCTGACACCTACATCTGAAAATATGTCGgtgagttatc ... cgtagtgcagATATGCAAGTTCTTCCTACAGCAGCGATGTCGATTTGGTAGTAACTGCCGC
EST: gi|149110259|gb|EE190315.2|EE190315
EST:     CAGGCGATGCAAGGATCTCATTTCTGACACCTACATCTGAAAATATGTCG                         ATATGCAAGTTCTTCCTACAGCAGCGATGTCGATTTGGTAGTAACTGCCGC
genomic: CAGGCGATGCAAGGATCTCATTTCTGACACCTACATCTGAAAATATGTCGgtgagttatc ... cgtagtgcagATATGCAAGTTCTTCCTACAGCAGCGATGTCGATTTGGTAGTAACTGCCGC
EST: gi|148932219|gb|EC875717.2|EC875717
EST:     CAGGCGATGCAAGGATCTCATTTCTGACACCTACATCTGAAAATATGTCG                         ATATGCAAGTTCTTCCTACAGCAGCGATGTCGATTTGGTAGTAACTGCCGC
genomic: CAGGCGATGCAAGGATCTCATTTCTGACACCTACATCTGAAAATATGTCGgtgagttatc ... cgtagtgcagATATGCAAGTTCTTCCTACAGCAGCGATGTCGATTTGGTAGTAACTGCCGC
EST: gi|148999333|gb|EE036269.2|EE036269
EST:     CAGGCGATGCAAGGATCTCATTTCTGACACCTACATCTGAAAATATGTCG                         ATATGCAAGTTCTTCCTACAGCAGCGATGTCGATTTGGTAGTAACTGCCGC
genomic: CAGGCGATGCAAGGATCTCATTTCTGACACCTACATCTGAAAATATGTCGgtgagttatc ... cgtagtgcagATATGCAAGTTCTTCCTACAGCAGCGATGTCGATTTGGTAGTAACTGCCGC

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), 48 (downstream exon)
Score: 100

GCACAACAATGGGCGCTGGTATAATGGATGCATTATAGGCTTTGAAGGTTCAGGCGATGCAAGGATCTCATTTCTGACACCTACATCTGAAAATATGTCGgtgagttatc ... cgtagtgcagATATGCAAGTTCTTCCTACAGCAGCGATGTCGATTTGGTAGTAACTGCCGCATGTCTCATG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 43

GCACAACAATGGGCGCTGGTATAATGGATGCATTATAGGCTTTGAAGGTTCAGGCGATGCAAGGATCTCATTTCTGACACCTACATCTGAAAATATGTCGgtgagttatc ... cgtagtgcagATATGCAAGTTCTTCCTACAGCAGCGATGTCGATTTGGTAGTAACTGCCGCATGTCTCATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 54

GCACAACAATGGGCGCTGGTATAATGGATGCATTATAGGCTTTGAAGGTTCAGGCGATGCAAGGATCTCATTTCTGACACCTACATCTGAAAATATGTCGgtgagttatc ... cgtagtgcagATATGCAAGTTCTTCCTACAGCAGCGATGTCGATTTGGTAGTAACTGCCGCATGTCTCATG


Block sizes: 49 (upstream exon), 41 (downstream exon)
Score: 44

GCACAACAATGGGCGCTGGTATAATGGATGCATTATAGGCTTTGAAGGTTCAGGCGATGCAAGGATCTCATTTCTGACACCTACATCTGAAAATATGTCGgtgagttatc ... cgtagtgcagATATGCAAGTTCTTCCTACAGCAGCGATGTCGATTTGGTAGTAACTGCCGCATGTCTCATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtatgcgccattattatgaacaaactaactaatacaaatctggccgtagtgcagATATGCAAGTTCTTCCTACAGCAGCGATGTCGATTTGGTAGTAACTGCCGCATGTCTCATG
          attattatgaacaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctggcataattttctgcttgctaacacaaatataatgattggagtgtatgcgccattattatgaacaaactaactaatacaaatctggccgtagtgcagATATGCAAGTTCTTCCTACAGCAGCGATGTCGATTTGGTAGTAACTGCCGCATGTCTCATG

- - - - - - - -tgcttgc
- - - - - - - - - - - - acacaaa
- - - - - - - - - - - - - - - - - -atgattg
- - - - - - - - - - - - - - - - - - - - - - -tgtatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atacaaa