ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

TCCCGCTGATCTAAAATACATTGATCCAACATATATGGTTCGGGCCTGCCGGGCAAATGCATCTGATGCTATTCTCTGCACCGTACTTGGGCAAAATGCTgtaagttgatttcttttcattttgtgttagtattcatttcaatgcaagagtaggatttttacagaacaaaattgtatggatgtcctttag

Basic information

species	Zea mays
transcript	GRMZM2G127717_T01
intron #	13
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G127717_T01 (Zea mays), 5'ss of exon 13
lower sequence: LOC_Os09g24910.2 (Oryza sativa), 5'ss of exon 13

TCCCGCTGATCTAAAATACATTGATCCAACATATATGGTTCGGGCCTGCCGGGCAAATGCATCTGATGCTATTCTCTGCACCGTACTTGGGCAAAATGCTgtaagttgatttcttttcattttgtgttagtattcatttca---atgcaagagtag--------gatttttacagaacaaaattgtatggatgtcctttag----------
||| |||||| |||||||||||||||| ||||||||||| |||||||| || || |||||||||||||||||  | ||||| |||||||| ||||||||||| ||||    | ||| |  |||||  |  |||    ||||   ||| | || ||         ||| |||    |     | ||| || |  ||   | |          
TCCAGCTGATGTAAAATACATTGATCCGACATATATGGTCCGGGCCTGTCGTGCGAATGCATCTGATGCTATCTTGTGCACTGTACTTGGACAAAATGCTgtgagttcgcgtttttcctgtttgtccttctatatccttcacagatgtatgaatatcatttatcgatctttttgaattttgagtgtttgaaaatcgaatggttttctgtag

upper sequence: GRMZM2G127717_T01 (Zea mays), 5'ss of exon 13
lower sequence: Vv14s0108g00540.t01 (Vitis vinifera), 5'ss of exon 13

TCCCGCTGATCTAAAATACATTGATCCAACATATATGGTTCGGGCCTGCCGGGCAAATGCATCTGATGCTATTCTCTGCACCGTACTTGGGCAAAATGCTgtaagttgatttcttttcattttgtgttagtattcatttcaatgcaagagtaggatttttacagaacaaaattgtatggatgtcctttag
||| |||||| | |||||||||||||| || |||||| |||| || || || |||||||||||||||||| |||| ||||| || ||||| || ||||||||||||  ||   | |    ||  || || | || |  |  || || |  ||  ||  |   | |  |   ||| |              
TCCAGCTGATGTTAAATACATTGATCCCACTTATATGATTCGAGCGTGTCGAGCAAATGCATCTGATGCTGTTCTTTGCACTGTTCTTGGCCAGAATGCTgtaagtgtatgaatatc---ttcatgataatcttgagat-gatccaggtctacaatggtggtatatgatccttgcag-------------

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|17929608|gb|BM266568.1|BM266568

EST:     GGCAAAATGCATCTGATGCTATTCTCTGCACCGTACTTGGGCAAAATGCT                         GTCCATGGAGCATTTGCTGGGTTCAGTGGCATCACGTCAGGTGTTTGCAAC
genomic: GGC-AAATGCATCTGATGCTATTCTCTGCACCGTACTTGGGCAAAATGCTgtaagttgat ... tgtcctttagGTCCATGGAGCATTTGCTGGGTTCAGTGGCATCACGTCAGGTGTTTGCAAC

EST: gi|12968916|gb|BG265757.1|BG265757

EST:     GGGCAAATGCATCTGACGCTATTCTCTGCACCGTACTTGGGCAAAACGCT                         GTCCATGGAGCATTTGCTGGGTTCAGTGGCATCACGTCAGGTGTTTGCAAC
genomic: GGGCAAATGCATCTGATGCTATTCTCTGCACCGTACTTGGGCAAAATGCTgtaagttgat ... tgtcctttagGTCCATGGAGCATTTGCTGGGTTCAGTGGCATCACGTCAGGTGTTTGCAAC

EST: gi|56382617|gb|CV985286.1|CV985286

EST:     GGGCAAATGCATCTGATGCTATTCTCTGCACCGTACTTGGGCAAAATGCT                         GTCCATGGAGCATTTGCTGGGTTCAGTGGCATCACGTCAGGTGTTTGCAAC
genomic: GGGCAAATGCATCTGATGCTATTCTCTGCACCGTACTTGGGCAAAATGCTgtaagttgat ... tgtcctttagGTCCATGGAGCATTTGCTGGGTTCAGTGGCATCACGTCAGGTGTTTGCAAC

EST: gi|31361900|gb|CD446257.1|CD446257

EST:     GGGCAAATGCATCTGATGCTATTCTTTGCACCGTACTTGGGCAAAATGCT                         GTCCATGGAGCATTTGCTGGGTTCAGTGGCATCACGTCAGGTGTTTGCAAC
genomic: GGGCAAATGCATCTGATGCTATTCTCTGCACCGTACTTGGGCAAAATGCTgtaagttgat ... tgtcctttagGTCCATGGAGCATTTGCTGGGTTCAGTGGCATCACGTCAGGTGTTTGCAAC

EST: gi|31361085|gb|CD445442.1|CD445442

EST:     GGGCAAATGCATCTGATGCTATTCTCTGCACCGTACTTGGGCAAAATGCT                         GTCCATGGAGCATTTGCTGGGTTCAGTGGCATCACGTCAGGTGTTTGCAAC
genomic: GGGCAAATGCATCTGATGCTATTCTCTGCACCGTACTTGGGCAAAATGCTgtaagttgat ... tgtcctttagGTCCATGGAGCATTTGCTGGGTTCAGTGGCATCACGTCAGGTGTTTGCAAC

EST: gi|76283550|gb|DV023118.1|DV023118

EST:     GGGCAAATGCATCTGATGCTATTCTCTGCACCGTACTTGGGCAAAATGCT                         GTCCATGGAGCATTTGCTGGGTTCAGTGGCATCACGTCAGGTGTTTGCAAC
genomic: GGGCAAATGCATCTGATGCTATTCTCTGCACCGTACTTGGGCAAAATGCTgtaagttgat ... tgtcctttagGTCCATGGAGCATTTGCTGGGTTCAGTGGCATCACGTCAGGTGTTTGCAAC

EST: gi|50339174|gb|CO534300.1|CO534300

EST:     GCACCGTACTTGGGCAAAATGCT                         GTCCATGGAGCATTTGCTGGGTTCAGTGGCATCACGTCAGGTGTTTGCAAC
genomic: GCACCGTACTTGGGCAAAATGCTgtaagttgat ... tgtcctttagGTCCATGGAGCATTTGCTGGGTTCAGTGGCATCACGTCAGGTGTTTGCAAC

EST: gi|32836430|gb|CD976108.1|CD976108

EST:     ACTTGGGCAAAATGCT                         GTCCATGGAGCATTTGCTGGGTTCAGTGGCATCACGTCAGGTGTTTGCAAC
genomic: ACTTGGGCAAAATGCTgtaagttgat ... tgtcctttagGTCCATGGAGCATTTGCTGGGTTCAGTGGCATCACGTCAGGTGTTTGCAAC

EST: gi|32932003|gb|CF036815.1|CF036815

EST:     GTACTTGGGCAAAATGCT                         GTCCATGGAGCATTTGCTGGGTTCAGTGGCATCACGTCAGGTGTTTGCAAC
genomic: GTACTTGGGCAAAATGCTgtaagttgat ... tgtcctttagGTCCATGGAGCATTTGCTGGGTTCAGTGGCATCACGTCAGGTGTTTGCAAC

EST: gi|18164682|gb|BM334521.1|BM334521

EST:     GGGCAAATGCATCTGATGCTATTCTCTGCACCGTACTTGGGCAAAATGCT                         GTCCATGGAGCATTTGCTGGGTTCAGTGGCATCACGTCAGGTGTTTGCAAC
genomic: GGGCAAATGCATCTGATGCTATTCTCTGCACCGTACTTGGGCAAAATGCTgtaagttgat ... tgtcctttagGTCCATGGAGCATTTGCTGGGTTCAGTGGCATCACGTCAGGTGTTTGCAAC

EST: gi|78021223|gb|DV489610.1|DV489610

EST:     GGGCAAATGCATCTGACGCTATTCTCTGCACCGTACTTGGGCAAAACGCT                         GTCCATGGAGCATTTGCTGGGTTCAGTGGCATCACGTCAGGTGTTTGCAAC
genomic: GGGCAAATGCATCTGATGCTATTCTCTGCACCGTACTTGGGCAAAATGCTgtaagttgat ... tgtcctttagGTCCATGGAGCATTTGCTGGGTTCAGTGGCATCACGTCAGGTGTTTGCAAC

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), 41 (downstream exon)
Score: 58

TCCCGCTGATCTAAAATACATTGATCCAACATATATGGTTCGGGCCTGCCGGGCAAATGCATCTGATGCTATTCTCTGCACCGTACTTGGGCAAAATGCTgtaagttgat ... tgtcctttagGTCCATGGAGCATTTGCTGGGTTCAGTGGCATCACGTCAGGTGTTTGCAACACACATTATGTCTACCTTCCCATCACAGAGGTCATTACAACACCAAAGC

Block sizes: 49 (upstream exon), 40 (downstream exon)
Score: 21

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 23