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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccagtgcatcttattaaacttgtcagccatattagactgtatggtcatactaatcattgtatcatgagaacttaccaatttctctttttccttattacagGAAGATGGCTGGCGGCTTCAGGGTACTTCATCTGGTCAGGCCCTTTCTGGCTTTCTTGCCAGAGGTGCAGAGCGCGGATAGGAAGATACCATTCAGAGAA

Basic information

species Zea mays
transcript GRMZM2G130987_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G130987_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g11440.1 (Oryza sativa), 3'ss of exon 1
ccagtgcatcttattaaacttgtcagccatat-tagactgtatggtc-atactaatcattgtatcatgagaacttaccaatttctctttttccttattacagGAA--GATGGCTGGCGGCTTCAGGGTACTTCATCTGGTCAGGCCCTTTCTGGCTTTCTTGCCAGAGGTGCAGAGCGCGGATAGGAAGATACCATTCAGAGAA
  |||      ||  ||  |||  |    | |  |      ||| |  ||| |  |   || ||  |   || |    |  |  | |||| | |  | |||||||  ||||||||| ||||| |||||| | ||||| |||||||| |||||||||||| |||| || || ||||| || |||||||| |||||||| ||||  
--agtctgaactaccaagtttgaaatttttttacaagacacatgttttataattttgtgtgcattgtacaaaatcttgacctatttttttgcttggtcacagGAAAAGATGGCTGGTGGCTTTAGGGTATTGCATCTTGTCAGGCCTTTTCTGGCTTTCCTGCCTGAAGTACAGAGTGCTGATAGGAAAATACCATTTAGAG--
















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|31361484|gb|CD445841.1|CD445841
EST:     GGCGTCGCGCTCTGGTCGTCGTCGGCCGG                         GAAGATGGCTGGCGGCTTCAGGGTACTGCATCTGGTCAGGCCCTTTCTGGC
genomic: GGCGTCGCGCTCTGGTCGTCGTCGGCCGGgtaaatctgc ... cttattacagGAAGATGGCTGGCGGCTTCAGGGTACTTCATCTGGTCAGGCCCTTTCTGGC
EST: gi|26456843|gb|CA828426.1|CA828426
EST:     GCTCTGGTCG-CGTCGG-CGG                         GAAGATGG-TGGCGGCTTCAGGGTACTTCATCTGGTCAGGCCCTTTCTGGC
genomic: GCTCTGGTCGTCGTCGGCCGGgtaaatctgc ... cttattacagGAAGATGGCTGGCGGCTTCAGGGTACTTCATCTGGTCAGGCCCTTTCTGGC
EST: gi|211074844|gb|FK968210.1|FK968210
EST:     GGCGAAGCTTCTGCCCTCCCCGGCGTCGGGCTCTGGTCGTCGTCGGCCGG                         GAAGATGGCTGGCGGCTTCAGGGTACTTCATCTGGTCAGGCCCTTTCTGGC
genomic: GGCGAAGCTTCTGCCCTCCCCGGCGTCGCGCTCTGGTCGTCGTCGGCCGGgtaaatctgc ... cttattacagGAAGATGGCTGGCGGCTTCAGGGTACTTCATCTGGTCAGGCCCTTTCTGGC
EST: gi|211074839|gb|FK968205.1|FK968205
EST:     GGCGAAGCTTCTGCCCTCCCCGGCGTCGCGCTCTGGTCGTCGTCGGCCGG                         GAAGATGGCTGGCGGCTTCAGGGTACTTCATCTGGTCAGGCCCTTTCTGGC
genomic: GGCGAAGCTTCTGCCCTCCCCGGCGTCGCGCTCTGGTCGTCGTCGGCCGGgtaaatctgc ... cttattacagGAAGATGGCTGGCGGCTTCAGGGTACTTCATCTGGTCAGGCCCTTTCTGGC
EST: gi|6021529|gb|AW066457.1|AW066457
EST:     GGCGAAGCTTCTGCCCTCCCCGGCGTCGGGCTCTGGTCGTCGTCGGCCGG                         GAAGATGGCTGGCGGCTTCAGGGTACTTCATCTGGTCAGGCCCTTTCTGGC
genomic: GGCGAAGCTTCTGCCCTCCCCGGCGTCGCGCTCTGGTCGTCGTCGGCCGGgtaaatctgc ... cttattacagGAAGATGGCTGGCGGCTTCAGGGTACTTCATCTGGTCAGGCCCTTTCTGGC
EST: gi|149111354|gb|EE294857.2|EE294857
EST:     GGCGAAGCTTCTGCCCTCCCCGGCGTCGCGCTCTGGTCGTCGTCGGCCGG                         GAAGATGGCTGGCGGCTTCAGGGTACTTCATCTGGTCAGGCCCTTTCTGGC
genomic: GGCGAAGCTTCTGCCCTCCCCGGCGTCGCGCTCTGGTCGTCGTCGGCCGGgtaaatctgc ... cttattacagGAAGATGGCTGGCGGCTTCAGGGTACTTCATCTGGTCAGGCCCTTTCTGGC
EST: gi|15198869|gb|BI423525.1|BI423525
EST:     CGCGCTCTGGTCGTCGTCGGCCGG                         GAAGATGGCTGGCGGCTTCAGGGTACTGCATCTGGTCAGGCCCTTTCTGGC
genomic: CGCGCTCTGGTCGTCGTCGGCCGGgtaaatctgc ... cttattacagGAAGATGGCTGGCGGCTTCAGGGTACTTCATCTGGTCAGGCCCTTTCTGGC
EST: gi|31350934|gb|CD435291.1|CD435291
EST:     GGCGTCGCGCTCTGGTCGTCGTCGGCCGG                         GAAGATGGCTGGCGGCTTCAGGGTACTGCATCTGGTCAGGCCCTTTCTGGC
genomic: GGCGTCGCGCTCTGGTCGTCGTCGGCCGGgtaaatctgc ... cttattacagGAAGATGGCTGGCGGCTTCAGGGTACTTCATCTGGTCAGGCCCTTTCTGGC
EST: gi|20507033|gb|BQ279454.1|BQ279454
EST:     GTCGGGCTCTGGTCGTCGTCGGCCGG                         GAAGATGGCTGGCGGCTTCAGGGTACTTCATCTGGTCAGGCCCTTTCTGGC
genomic: GTCGCGCTCTGGTCGTCGTCGGCCGGgtaaatctgc ... cttattacagGAAGATGGCTGGCGGCTTCAGGGTACTTCATCTGGTCAGGCCCTTTCTGGC
EST: gi|211074842|gb|FK968208.1|FK968208
EST:     GGCGAAGCTTCTGCCCTCCCCGGCGTCGGGCTCTGGTCGTCGTCGGCCGG                         GAAGATGGCTGGCGGCTTCAGGGTACTTCATCTGGTCAGGCCCTTTCTGGC
genomic: GGCGAAGCTTCTGCCCTCCCCGGCGTCGCGCTCTGGTCGTCGTCGGCCGGgtaaatctgc ... cttattacagGAAGATGGCTGGCGGCTTCAGGGTACTTCATCTGGTCAGGCCCTTTCTGGC
EST: gi|67035315|gb|CO463848.1|CO463848
EST:     GGCGAAGCTTCTGCCCTCCCCGGCGTCGCGCTCTGGTCGTCGTCGGCCGG                         GAAGATGGCTGGCGGCTTCAGGGTACTTCATCTGGTCAGGCCCTTTCTGGC
genomic: GGCGAAGCTTCTGCCCTCCCCGGCGTCGCGCTCTGGTCGTCGTCGGCCGGgtaaatctgc ... cttattacagGAAGATGGCTGGCGGCTTCAGGGTACTTCATCTGGTCAGGCCCTTTCTGGC
EST: gi|211074841|gb|FK968207.1|FK968207
EST:     GGCGAAGCTTCTGCCCTCCCCGGCGTCGCGCTCTGGTCGTCGTCGGCCGG                         GAAGATGGCTGGCGGCTTCAGGGTACTTCATCTGGTCAGGCCCTTTCTGGC
genomic: GGCGAAGCTTCTGCCCTCCCCGGCGTCGCGCTCTGGTCGTCGTCGGCCGGgtaaatctgc ... cttattacagGAAGATGGCTGGCGGCTTCAGGGTACTTCATCTGGTCAGGCCCTTTCTGGC
EST: gi|149008958|gb|EE041174.2|EE041174
EST:     GGCGAAGCTTCTGCCCTCCCCGGCGTCGCGCTCTGGTCGTCGTCGGCCGG                         GAAGATGGCTGGCGGCTTCAGGGTACTTCATCTGGTCAGGCCCTTTCTGGC
genomic: GGCGAAGCTTCTGCCCTCCCCGGCGTCGCGCTCTGGTCGTCGTCGGCCGGgtaaatctgc ... cttattacagGAAGATGGCTGGCGGCTTCAGGGTACTTCATCTGGTCAGGCCCTTTCTGGC
EST: gi|67037304|gb|CO464154.1|CO464154
EST:     GGCGAAGCTTCTGCCCTCCCCGGCGTCGCGCTCTGGTCGTCGTCGGCCGG                         GAAGATGGCTGGCGGCTTCAGGGTACTTCATCTGGTCAGGCCCTTTCTGGC
genomic: GGCGAAGCTTCTGCCCTCCCCGGCGTCGCGCTCTGGTCGTCGTCGGCCGGgtaaatctgc ... cttattacagGAAGATGGCTGGCGGCTTCAGGGTACTTCATCTGGTCAGGCCCTTTCTGGC
EST: gi|67029660|gb|CO458409.1|CO458409
EST:     GGCGAAGCTTCTGCCCTCCCCGGCGTCGGGCTCTGGTCCTCGTCGGCCGG                         GAAGATGGCTGGCGGCTTCAGGGTACTTCATCTGGTCAGGCCCTTTCTGGC
genomic: GGCGAAGCTTCTGCCCTCCCCGGCGTCGCGCTCTGGTCGTCGTCGGCCGGgtaaatctgc ... cttattacagGAAGATGGCTGGCGGCTTCAGGGTACTTCATCTGGTCAGGCCCTTTCTGGC
EST: gi|67042883|gb|CO469138.1|CO469138
EST:     GGCGAAGCTTCTGCCCTCCCCGGCGTCGGGCTCTGGTCGTCGTCTGCCGG                         CAAGATGGCTGGCGGCTTCAGGGTACTTCATCTGGTCAGGCCCTTTCTGGC
genomic: GGCGAAGCTTCTGCCCTCCCCGGCGTCGCGCTCTGGTCGTCGTCGGCCGGgtaaatctgc ... cttattacagGAAGATGGCTGGCGGCTTCAGGGTACTTCATCTGGTCAGGCCCTTTCTGGC
EST: gi|149109194|gb|EE190067.2|EE190067
EST:     GGCGAAGCTTCTGCCCTCCCCGGCGTCGCGCTCTGGTCGTCGTCGGCCGG                         GAAGATGGCTGGCGGCTTCAGGGTACTTCATCTGGTCAGGCCCTTTCTGGC
genomic: GGCGAAGCTTCTGCCCTCCCCGGCGTCGCGCTCTGGTCGTCGTCGGCCGGgtaaatctgc ... cttattacagGAAGATGGCTGGCGGCTTCAGGGTACTTCATCTGGTCAGGCCCTTTCTGGC
EST: gi|148953634|gb|EC898991.2|EC898991
EST:     GGCGAAGCTTCTGCCCTCCCCGGCGTCGCGCTCTGGTCGTCGTCGGCCGG                         GAAGATGGCTGGCGGCTTCAGGGTACTTCATCTGGTCAGGCCCTTTCTGGC
genomic: GGCGAAGCTTCTGCCCTCCCCGGCGTCGCGCTCTGGTCGTCGTCGGCCGGgtaaatctgc ... cttattacagGAAGATGGCTGGCGGCTTCAGGGTACTTCATCTGGTCAGGCCCTTTCTGGC
EST: gi|148939934|gb|EC884655.2|EC884655
EST:     GGCGAAGCTTCTGCCCTCCCCGGCGTCGCGCTCTGGTCGTCGTCGGCCGG                         GAAGATGGCTGGCGGCTTCAGGGTACTTCATCTGGTCAGGCCCTTTCTGGC
genomic: GGCGAAGCTTCTGCCCTCCCCGGCGTCGCGCTCTGGTCGTCGTCGGCCGGgtaaatctgc ... cttattacagGAAGATGGCTGGCGGCTTCAGGGTACTTCATCTGGTCAGGCCCTTTCTGGC
EST: gi|32914742|gb|CF019554.1|CF019554
EST:     GGCGAAGCTTCTGCCCTCCCCGGCGTCGCGCTCTGGTCGTCGTCGGCCGG                         GAAGATGGCTGGCGGCTTCAGGGTACCTTCATCTGGTCAGGCCCTTTTTGT
genomic: GGCGAAGCTTCTGCCCTCCCCGGCGTCGCGCTCTGGTCGTCGTCGGCCGGgtaaatctgc ... cttattacagGAAGATGGCTGGCGGCTTCAGGGTA-CTTCATCTGGTCAGGCCCTTTCTGG
EST: gi|148936308|gb|EC880390.2|EC880390
EST:     GGCGAAGCTTCTGCCCTCCCCGGCGTCGCGCTCTGGTCGTCGTCGGCCGG                         GAAGATGGCTGGCGGCTTCAGGGTACTTCATCTGGTCAGGCCCTTTCTGGC
genomic: GGCGAAGCTTCTGCCCTCCCCGGCGTCGCGCTCTGGTCGTCGTCGGCCGGgtaaatctgc ... cttattacagGAAGATGGCTGGCGGCTTCAGGGTACTTCATCTGGTCAGGCCCTTTCTGGC
EST: gi|149113040|gb|EE295813.2|EE295813
EST:     GGCGAAGCTTCTGCCCTCCCCGGCGTCGCGCTCTGGTCGTCGTCGGCCGG                         GAAGATGGCTGGCGGCTTCAGGGTACTTCATCTGGTCAGGCCCTTTCTGGC
genomic: GGCGAAGCTTCTGCCCTCCCCGGCGTCGCGCTCTGGTCGTCGTCGGCCGGgtaaatctgc ... cttattacagGAAGATGGCTGGCGGCTTCAGGGTACTTCATCTGGTCAGGCCCTTTCTGGC
EST: gi|31353192|gb|CD437549.1|CD437549
EST:     GGCGAACCTTCTGCCCTCCCCGGCGTCGCGCTCTGGTCGTCGTCGGCCGG                         GAAGATGGCTGGCGGCTTCAGGGTACTTCATCTGGTCAGGCCCTTTCTGGC
genomic: GGCGAAGCTTCTGCCCTCCCCGGCGTCGCGCTCTGGTCGTCGTCGGCCGGgtaaatctgc ... cttattacagGAAGATGGCTGGCGGCTTCAGGGTACTTCATCTGGTCAGGCCCTTTCTGGC
EST: gi|116822305|gb|EC865696.1|EC865696
EST:     CGANAGCTTCTGGCCCT-CCCGGCGTCGCGCTCTGGTCGTCGTCGGCCGG                         GAAGATGGCTGGCGGCTTCAGGATACTTCATGCTGGTCAGGCCCTTTCTGG
genomic: CGA-AGCTTCT-GCCCTCCCCGGCGTCGCGCTCTGGTCGTCGTCGGCCGGgtaaatctgc ... cttattacagGAAGATGGCTGGCGGCTTCAGGGTACTTCAT-CTGGTCAGGCCCTTTCTGG
EST: gi|31360614|gb|CD444971.1|CD444971
EST:     GGCGAAGCTTCTGCCCTCCCCGGCGTCGCGCTCTGGTCGTCGTCGGCCGG                         GAAGATGGCTGGCGGCTTCAGGGTACTTCATCTGGTCAGGCCCTTTCTGGC
genomic: GGCGAAGCTTCTGCCCTCCCCGGCGTCGCGCTCTGGTCGTCGTCGGCCGGgtaaatctgc ... cttattacagGAAGATGGCTGGCGGCTTCAGGGTACTTCATCTGGTCAGGCCCTTTCTGGC
EST: gi|148932797|gb|EE285481.2|EE285481
EST:     GGCGAAGCTTCTGCCCTCCCCGGCGTCGCGCTCTGGTCGTCGTCGGCCGG                         GAAGATGGCTGGCGGCTTCAGGGTACTTCATCTGGTCAGGCCCTTTCTGGC
genomic: GGCGAAGCTTCTGCCCTCCCCGGCGTCGCGCTCTGGTCGTCGTCGGCCGGgtaaatctgc ... cttattacagGAAGATGGCTGGCGGCTTCAGGGTACTTCATCTGGTCAGGCCCTTTCTGGC
EST: gi|211072106|gb|FK968195.1|FK968195
EST:     GGCGAAGCTTCTGCCCTCCCCGGCGTCGCGCTCTGGTCGTCGTCGGCCGG                         GAAGATGGCTGGCGGCTTCAGGGTACTTCATCTGGTCAGGCCCTTTCTGGC
genomic: GGCGAAGCTTCTGCCCTCCCCGGCGTCGCGCTCTGGTCGTCGTCGGCCGGgtaaatctgc ... cttattacagGAAGATGGCTGGCGGCTTCAGGGTACTTCATCTGGTCAGGCCCTTTCTGGC
EST: gi|31356381|gb|CD440738.1|CD440738
EST:     GGCGTCGCGCTCTGGTCGTCGTCGGCCGG                         GAAGATGGCTGGCGGCTTCAGGGTACTGCATCTGGTCAGGCCCTTTCTGGC
genomic: GGCGTCGCGCTCTGGTCGTCGTCGGCCGGgtaaatctgc ... cttattacagGAAGATGGCTGGCGGCTTCAGGGTACTTCATCTGGTCAGGCCCTTTCTGGC
EST: gi|211072113|gb|FK968202.1|FK968202
EST:     GGCGAAGCTTCTGCCCTCCCCGGCGTCGCGCTCTGGTCGTCGTCGGCCGG                         GAAGATGGCTGGCGGCTTCAGGGTACTTCATCTGGTCAGGCCCTTTCTGGC
genomic: GGCGAAGCTTCTGCCCTCCCCGGCGTCGCGCTCTGGTCGTCGTCGGCCGGgtaaatctgc ... cttattacagGAAGATGGCTGGCGGCTTCAGGGTACTTCATCTGGTCAGGCCCTTTCTGGC

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: 608

TCTCCTCTCATCTCCACCTCTCCTCCGGCTAGGGTGTTCACGCCTGCCGCGGCGAAGCTTCTGCCCTCCCCGGCGTCGCGCTCTGGTCGTCGTCGGCCGGgtaaatctgc ... cttattacagGAAGATGGCTGGCGGCTTCAGGGTACTTCATCTGGTCAGGCCCTTTCTGGCTTTCTTGCCAGAGGTGCAGAGCGCGGATAGGAAGATACCATTCAGAGAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 503

TCTCCTCTCATCTCCACCTCTCCTCCGGCTAGGGTGTTCACGCCTGCCGCGGCGAAGCTTCTGCCCTCCCCGGCGTCGCGCTCTGGTCGTCGTCGGCCGGgtaaatctgc ... cttattacagGAAGATGGCTGGCGGCTTCAGGGTACTTCATCTGGTCAGGCCCTTTCTGGCTTTCTTGCCAGAGGTGCAGAGCGCGGATAGGAAGATACCATTCAGAGAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 322

TCTCCTCTCATCTCCACCTCTCCTCCGGCTAGGGTGTTCACGCCTGCCGCGGCGAAGCTTCTGCCCTCCCCGGCGTCGCGCTCTGGTCGTCGTCGGCCGGgtaaatctgc ... cttattacagGAAGATGGCTGGCGGCTTCAGGGTACTTCATCTGGTCAGGCCCTTTCTGGCTTTCTTGCCAGAGGTGCAGAGCGCGGATAGGAAGATACCATTCAGAGAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 585

TCTCCTCTCATCTCCACCTCTCCTCCGGCTAGGGTGTTCACGCCTGCCGCGGCGAAGCTTCTGCCCTCCCCGGCGTCGCGCTCTGGTCGTCGTCGGCCGGgtaaatctgc ... cttattacagGAAGATGGCTGGCGGCTTCAGGGTACTTCATCTGGTCAGGCCCTTTCTGGCTTTCTTGCCAGAGGTGCAGAGCGCGGATAGGAAGATACCATTCAGAGAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catactaatcattgtatcatgagaacttaccaatttctctttttccttattacagGAAGATGGCTGGCGGCTTCAGGGTACTTCATCTGGTCAGGCCCTTTCTGGCTTTCTTGCCAGAGGTGCAGAGCGCGGATAGGAAGATACCATTCAGAGAA
                         cttaccaatttctctt  CT-rich tract
     taatcatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccagtgcatcttattaaacttgtcagccatattagactgtatggtcatactaatcattgtatcatgagaacttaccaatttctctttttccttattacagGAAGATGGCTGGCGGCTTCAGGGTACTTCATCTGGTCAGGCCCTTTCTGGCTTTCTTGCCAGAGGTGCAGAGCGCGGATAGGAAGATACCATTCAGAGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA