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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagcaggacgctttatttggtttgaacaagttgctgcctttatattccgacatgcttattccttcagaggatttgtgtattaacatggttgacttttcagCCCTCCCGCGATTGAAAGGCTTTCTGGAGGCGTCTTTGAGGAAGTTATTGTGACAAACTCCATCCTGCTGCCGGAAGACAAATGCTTCCCTCAGCTGACT

Basic information

species Zea mays
transcript GRMZM2G180863_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G180863_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os06g41360.1 (Oryza sativa), 3'ss of exon 7
tagcaggacgctttatttggtttgaacaagttgctgcctt-tatattccgacatgcttattccttcagaggatttgtgtattaacatggttgacttttcagCCCTCCCGCGATTGAAAGGCTTTCTGGAGGCGTCTTTGAGGAAGTTATTGTGACAAACTCCATCCTGCTGCCGGAAGACAAATGCTTCCCTCAGCTGACT
  |||  |    || |    ||  |        ||   || ||       |  |   |  |    || |     | | |   |  |    || |||| ||||||||| |||||||||||||| ||||||||| ||||||||||||||||||||||||||||||| |||||||| ||  ||||||||||||| ||| |||| 
-tgcaaaaattgttgtccttttgtattcctgcactattttgtaggcataaaagtaagtcgtttaccacacctactttttcccactagcactgtctttgcagCCCTCCTGCGATTGAAAGGCTCTCTGGAGGCATCTTTGAGGAAGTTATTGTGACAAACTCCATTCTGCTGCCAGAGCACAAATGCTTCCCCCAGTTGACA
















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|211097069|gb|FL027762.1|FL027762
EST:     CAGGAGGGAGCAGAAGCTGTATATGCTTGTTGTACACATGCTGTTTTCAG                         CCCTCCCGCGATTGAAAGGCTTTCTGGAGGCGTCTTTGAGGAAGTTATTGT
genomic: CAGGAGGGAGCAGAAGCTGTATATGCTTGTTGTACACATGCTGTTTTCAGgttttctagt ... gacttttcagCCCTCCCGCGATTGAAAGGCTTTCTGGAGGCGTCTTTGAGGAAGTTATTGT
EST: gi|60341300|gb|DN208273.1|DN208273
EST:     CAGGAGGGAGCAGAAGCTGTATATGCTTGTTGTACACATGCTGTATTCAG                         CCCTCCCGCGATTGAAAGGCTTTCTGGAGGCGTCTTTGAGGAAGTTATTGT
genomic: CAGGAGGGAGCAGAAGCTGTATATGCTTGTTGTACACATGCTGTTTTCAGgttttctagt ... gacttttcagCCCTCCCGCGATTGAAAGGCTTTCTGGAGGCGTCTTTGAGGAAGTTATTGT
EST: gi|149079722|gb|EE168724.2|EE168724
EST:     CAGGAGGGAGCAGAAGCTGTATATGCTTGTTGTACACATGCTGTTTTCAG                         CCCTCCCGCGATTGAAAGGCTTTCTGGAGGCGTCTTTGAGGAAGTTATTGT
genomic: CAGGAGGGAGCAGAAGCTGTATATGCTTGTTGTACACATGCTGTTTTCAGgttttctagt ... gacttttcagCCCTCCCGCGATTGAAAGGCTTTCTGGAGGCGTCTTTGAGGAAGTTATTGT
EST: gi|86465674|gb|DY232047.1|DY232047
EST:     TGTATATGCTTGTTGTACACATGCTGTTTTCAG                         CCCTCCCGCGATTGAAAGGCTTTCTGGAGGCGTCTTTGAGGAAGTTATTGT
genomic: TGTATATGCTTGTTGTACACATGCTGTTTTCAGgttttctagt ... gacttttcagCCCTCCCGCGATTGAAAGGCTTTCTGGAGGCGTCTTTGAGGAAGTTATTGT
EST: gi|71770133|gb|DR968070.1|DR968070
EST:     CAGGAGGGAGCAGAAGCTGTATATGCTTGTTGTACACATGCTGTTTTCAG                         CCCTCCCGCGATTGAAAGGCTTTCTGGAGGCGTCTTTGAGGAAGTTATTGT
genomic: CAGGAGGGAGCAGAAGCTGTATATGCTTGTTGTACACATGCTGTTTTCAGgttttctagt ... gacttttcagCCCTCCCGCGATTGAAAGGCTTTCTGGAGGCGTCTTTGAGGAAGTTATTGT
EST: gi|211094604|gb|FL027759.1|FL027759
EST:     CAGGAGGGAGCAGAAGCTGTATATGCTTGTTGTACACATGCTGTTTTCAG                         CCCTCCCGCGATTGAWAGGCTTTCTGGAGGCGTCTTTGAGGAAGTTATTGT
genomic: CAGGAGGGAGCAGAAGCTGTATATGCTTGTTGTACACATGCTGTTTTCAGgttttctagt ... gacttttcagCCCTCCCGCGATTGAAAGGCTTTCTGGAGGCGTCTTTGAGGAAGTTATTGT
EST: gi|149006975|gb|EE040194.2|EE040194
EST:     CAGGAGGGAGCAGAAGCTGTATATGCTTGTTGTACACATGCTGTTTTCAG                         CCCTCCCGCGATTGAAAGGCTTTCTGGAGGCGTCTTTGAGGAAGTTATTGT
genomic: CAGGAGGGAGCAGAAGCTGTATATGCTTGTTGTACACATGCTGTTTTCAGgttttctagt ... gacttttcagCCCTCCCGCGATTGAAAGGCTTTCTGGAGGCGTCTTTGAGGAAGTTATTGT
EST: gi|149004709|gb|EE039202.2|EE039202
EST:     CAGGAGGGAGCAGAAGCTGTATATGCTTGTTGTACACATGCTGTTTTCAG                         CCCTCCCGCGATTGAAAGGCTTTCTGGAGGCGTCTTTGAGGAAGTTATTGT
genomic: CAGGAGGGAGCAGAAGCTGTATATGCTTGTTGTACACATGCTGTTTTCAGgttttctagt ... gacttttcagCCCTCCCGCGATTGAAAGGCTTTCTGGAGGCGTCTTTGAGGAAGTTATTGT
EST: gi|50325134|gb|CO520260.1|CO520260
EST:     CAGGAGGGAGCAGAAGCTGTATATGCTTGTTGTACACATGCTGTTTTCAG                         CCCTCCCGCGATTGAAAGGCTTTCTGGAGGCGTCTTTGAGGAAGTTATTGT
genomic: CAGGAGGGAGCAGAAGCTGTATATGCTTGTTGTACACATGCTGTTTTCAGgttttctagt ... gacttttcagCCCTCCCGCGATTGAAAGGCTTTCTGGAGGCGTCTTTGAGGAAGTTATTGT
EST: gi|60358780|gb|DN225753.1|DN225753
EST:     CAGGAGGGAGCAGAAGCTGTATATGCTTGTTGTACACATGCTGTTTTCAG                         CCCTCCCGCGATTGAAAGGCTTTCTGGAGGCGTCTTTGAGGAAGTTATTGT
genomic: CAGGAGGGAGCAGAAGCTGTATATGCTTGTTGTACACATGCTGTTTTCAGgttttctagt ... gacttttcagCCCTCCCGCGATTGAAAGGCTTTCTGGAGGCGTCTTTGAGGAAGTTATTGT
EST: gi|32924137|gb|CF028949.1|CF028949
EST:     ACACATGCTGTTTTCAG                         CCCTCCCGCGATTGAAAGGCTTTCTGGAGGCGTCTTTGAGGAAGTTATTGT
genomic: ACACATGCTGTTTTCAGgttttctagt ... gacttttcagCCCTCCCGCGATTGAAAGGCTTTCTGGAGGCGTCTTTGAGGAAGTTATTGT
EST: gi|148947743|gb|EC893226.2|EC893226
EST:     CAGGAGGGAGCAGAAGCTGTATATGCTTGTTGTACACATGCTGTTTTCAG                         CCCTCCCGCGATTGAAAGGCTTTCTGGAGGCGTCTTTGAGGAAGTTATTGT
genomic: CAGGAGGGAGCAGAAGCTGTATATGCTTGTTGTACACATGCTGTTTTCAGgttttctagt ... gacttttcagCCCTCCCGCGATTGAAAGGCTTTCTGGAGGCGTCTTTGAGGAAGTTATTGT
EST: gi|91874827|gb|EB404784.1|EB404784
EST:     CAGGAGGGAGCAGAAGCTGTATATGCTTGTTGTACACATGCTGTTTTCAG                         CCCTCCCGCGATTGAAAGGCTTTCTGGAGGGGTCTTTGAGGAAGTTATTGT
genomic: CAGGAGGGAGCAGAAGCTGTATATGCTTGTTGTACACATGCTGTTTTCAGgttttctagt ... gacttttcagCCCTCCCGCGATTGAAAGGCTTTCTGGAGGCGTCTTTGAGGAAGTTATTGT
EST: gi|149088667|gb|EE177785.2|EE177785
EST:     CAGGAGGGAGCAGAAGCTGTATATGCTTGTTGTACACATGCTGTTTTCAG                         CCCTCCCGCGATTGAAAGGCTTTCTGGAGGCGTCTTTGAGGAAGTTATTGT
genomic: CAGGAGGGAGCAGAAGCTGTATATGCTTGTTGTACACATGCTGTTTTCAGgttttctagt ... gacttttcagCCCTCCCGCGATTGAAAGGCTTTCTGGAGGCGTCTTTGAGGAAGTTATTGT
EST: gi|211094605|gb|FL027760.1|FL027760
EST:     CAGGAGGGAGCAGAAGCT-TATATGCTTGTTGTACACATGCTGTTTTCAG                         CCCTCCCGCGATTGAAAGGCTTTCTGGAGGCGTCTTTGAGGAAGTTATTGT
genomic: CAGGAGGGAGCAGAAGCTGTATATGCTTGTTGTACACATGCTGTTTTCAGgttttctagt ... gacttttcagCCCTCCCGCGATTGAAAGGCTTTCTGGAGGCGTCTTTGAGGAAGTTATTGT
EST: gi|24769265|gb|CA404394.1|CA404394
EST:     CAGGAGGGAGCAGAAGCTGTATATGCTTGTTGTACACATGCTGTTTTCAG                         CCCTCCCGCGATTGAAAGGCTTTCTGGAGGCGTCTTTGAGGAAGTTATTGT
genomic: CAGGAGGGAGCAGAAGCTGTATATGCTTGTTGTACACATGCTGTTTTCAGgttttctagt ... gacttttcagCCCTCCCGCGATTGAAAGGCTTTCTGGAGGCGTCTTTGAGGAAGTTATTGT
EST: gi|31354391|gb|CD438748.1|CD438748
EST:     CAGGAGGGAGCAGAAGCTGTATATGCTTGTTGTACACATGCTGTTTTCAG                         CCCTCCCGCGATTGAA
genomic: CAGGAGGGAGCAGAAGCTGTATATGCTTGTTGTACACATGCTGTTTTCAGgttttctagt ... gacttttcagCCCTCCCGCGATTGAA
EST: gi|50339734|gb|CO534860.1|CO534860
EST:     CAGGAGGGAGCAGAAGCTGTATATGCTTGTTGTACACATGCTGTTTTCAG                         CCCTCCCGCGATTGAAAGGCTTTCTGGAGGCGTCTTTGAGGAAGTTATTGT
genomic: CAGGAGGGAGCAGAAGCTGTATATGCTTGTTGTACACATGCTGTTTTCAGgttttctagt ... gacttttcagCCCTCCCGCGATTGAAAGGCTTTCTGGAGGCGTCTTTGAGGAAGTTATTGT
EST: gi|6021970|gb|AW066898.1|AW066898
EST:     ATGCTGTTTTCAG                         CCCTCCCGCGATTGAAAGGCTTTCTGGAGGCGTCTTTGAGGAAGTTATTGT
genomic: ATGCTGTTTTCAGgttttctagt ... gacttttcagCCCTCCCGCGATTGAAAGGCTTTCTGGAGGCGTCTTTGAGGAAGTTATTGT
EST: gi|32929555|gb|CF034367.1|CF034367
EST:     ACACATGCTGTTTTCAG                         CCCTCCCGCGATTGAAAGGCTTTCTGGAGGCGTCTTTGAGGAAGTTATTGT
genomic: ACACATGCTGTTTTCAGgttttctagt ... gacttttcagCCCTCCCGCGATTGAAAGGCTTTCTGGAGGCGTCTTTGAGGAAGTTATTGT
EST: gi|50322471|gb|CO517597.1|CO517597
EST:     CAGGAGGGAGCAGAAGCTGTATATGCTTGTTGTACACATGCTGTTTTCAG                         CCCTCCCGCGATTGAAAGGCTTTCTGGAGGCGTCTTTGAGGAAGTTATTGT
genomic: CAGGAGGGAGCAGAAGCTGTATATGCTTGTTGTACACATGCTGTTTTCAGgttttctagt ... gacttttcagCCCTCCCGCGATTGAAAGGCTTTCTGGAGGCGTCTTTGAGGAAGTTATTGT

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: 114

GGACAATCACTAGCGCAGCGGCTTTGTTAAAGCAGGAGGGAGCAGAAGCTGTATATGCTTGTTGTACACATGCTGTTTTCAGgttttctagt ... gacttttcagCCCTCCCGCGATTGAAAGGCTTTCTGGAGGCGTCTTTGAGGAAGTTATTGTGACAAACTCCATCCTGCTGCCGGAAGACAAATGCTTCCCTCAGCTGACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 204

GGACAATCACTAGCGCAGCGGCTTTGTTAAAGCAGGAGGGAGCAGAAGCTGTATATGCTTGTTGTACACATGCTGTTTTCAGgttttctagt ... gacttttcagCCCTCCCGCGATTGAAAGGCTTTCTGGAGGCGTCTTTGAGGAAGTTATTGTGACAAACTCCATCCTGCTGCCGGAAGACAAATGCTTCCCTCAGCTGACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 158

GGACAATCACTAGCGCAGCGGCTTTGTTAAAGCAGGAGGGAGCAGAAGCTGTATATGCTTGTTGTACACATGCTGTTTTCAGgttttctagt ... gacttttcagCCCTCCCGCGATTGAAAGGCTTTCTGGAGGCGTCTTTGAGGAAGTTATTGTGACAAACTCCATCCTGCTGCCGGAAGACAAATGCTTCCCTCAGCTGACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 128

GGACAATCACTAGCGCAGCGGCTTTGTTAAAGCAGGAGGGAGCAGAAGCTGTATATGCTTGTTGTACACATGCTGTTTTCAGgttttctagt ... gacttttcagCCCTCCCGCGATTGAAAGGCTTTCTGGAGGCGTCTTTGAGGAAGTTATTGTGACAAACTCCATCCTGCTGCCGGAAGACAAATGCTTCCCTCAGCTGACT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccgacatgcttattccttcagaggatttgtgtattaacatggttgacttttcagCCCTCCCGCGATTGAAAGGCTTTCTGGAGGCGTCTTTGAGGAAGTTATTGTGACAAACTCCATCCTGCTGCCGGAAGACAAATGCTTCCCTCAGCTGACT
                                               cttttc  CT-rich tract
                                tattaacat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagcaggacgctttatttggtttgaacaagttgctgcctttatattccgacatgcttattccttcagaggatttgtgtattaacatggttgacttttcagCCCTCCCGCGATTGAAAGGCTTTCTGGAGGCGTCTTTGAGGAAGTTATTGTGACAAACTCCATCCTGCTGCCGGAAGACAAATGCTTCCCTCAGCTGACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA