ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GCGAGGGCATGCTCGCTGGCGAGATGAAGCACGGGCCGCTGGCCCTCGTGGACGAGAACCTCCCCATCATTGTCATTGCGACCCGCGACGCGTGCTTCAGgtaatgataaagaagcatgggcccagctttggttaccctttttggtagcaggaaaccaacctcttttcaaaacctcttgcag

Basic information

species	Zea mays
transcript	GRMZM2G005849_T03
intron #	8
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G005849_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os12g03720.1 (Oryza sativa), 5'ss of exon 9

GCGAGGGCATGCTCGCTGGCGAGATGAAGCACGGGCCGCTGGCCCTCGTGGACGAGAACCTCCCCATCATTGTCATTGCGACCCGCGACGCGTGCTTCAGgtaa---tgataaagaagcatgggcccagctttggttaccctttttggtagcaggaaaccaacctcttttcaaaacctcttgcag
|||| |||||||| ||||| || |||||||| || || || || || ||||| || ||||| || ||||| |||||||| || || || |||||||||||||||      |  | |  |    |  ||  ||   || |  ||  |  |   ||||   |  |      ||   |||||||||||
GCGAAGGCATGCTTGCTGGTGAAATGAAGCATGGACCACTTGCACTAGTGGATGAAAACCTTCCGATCATCGTCATTGCTACACGTGATGCGTGCTTCAGgtaagcgctttggacagactgcagagcacgttcattttcttttcatttttcaaggagttcctctaaacatcttcacctcttgcag

upper sequence: GRMZM2G005849_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os11g03900.1 (Oryza sativa), 5'ss of exon 9

GCGAGGGCATGCTCGCTGGCGAGATGAAGCACGGGCCGCTGGCCCTCGTGGACGAGAACCTCCCCATCATTGTCATTGCGACCCGCGACGCGTGCTTCAGgtaa---tgataaagaagcatgggcccagctttggttaccctttttggtagcaggaaaccaacctcttttcaaaacctcttgcag
|||| |||||||| ||||| || |||||||| || || || || || ||||| || ||||| || ||||| |||||||| || || || |||||||||||||||      |  | |  |    |  ||  ||   || |  ||  |  |   ||||   |  |      ||   |||||||||||
GCGAAGGCATGCTTGCTGGTGAAATGAAGCATGGACCACTTGCACTAGTGGATGAAAACCTTCCGATCATCGTCATTGCTACACGTGATGCGTGCTTCAGgtaagcgctttggacagactacagagcacgttcattttcttttcatttttcaaggagttcctctaaacatcttcacctcttgcag

upper sequence: GRMZM2G005849_T01 (Zea mays), 5'ss of exon 9
lower sequence: EDP02705 (Chlamydomonas reinhardtii), 5'ss of exon 16

---------------GCGAGGGCATGCTCGCTGGCGAGATGAAGCACGGGCCGCTGGCCCTCGTGGACGAGAACCTCCCCATCATTGTCATTGCGACCCG-CGACGCGT-GCTTCAGgtaatgataaagaagcatgggcccagcttt----ggttaccctttttggtagcaggaaaccaacctcttttcaaaacctcttgcag
               |||||||||| || || ||||||||||||||||| |||||||| || |||||| |  || | |||||| | ||||| || || ||  || |||  |   |||  |  |   | || ||  |||  |          ||  | |    |  |  | ||    | |     |  |||  |  ||  ||| 
TGGCCATCATCCACAGCGAGGGCATCCTGGCGGGCGAGATGAAGCACGGCCCGCTGGCGCTGGTGGACAAACACATGCCCATCGTCGTCATCGCCACGCGgtgaggcggagagccagaaagaggggaggatgcgggggggcgatgacaggcggcgagcaggctccgcgggagtttgctatataatgatcagga--tcaggca-

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|211507116|gb|FK960930.1|FK960930

EST:     GACGAGAACCTCCCCATCATTGTCATTGCGACCCGCGACGCGTGCTTCAG                         CAAGCAGCAGTCGGTGATCCAACAGCTCCTCTCGCGCAGGGGGCGCCTGAT
genomic: GACGAGAACCTCCCCATCATTGTCATTGCGACCCGCGACGCGTGCTTCAGgtaatgataa ... cctcttgcagCAAGCAGCAGTCGGTGATCCAACAGCTCCTCTCGCGCAGGGGGCGCCTGAT

EST: gi|7216484|gb|AW562606.1|AW562606

EST:     GACGAGAACCTCCCCATCATTGTCATTGCGACTCGCGACGCGTGCTTCAG                         CAAGCAGCAGTCGGTGATCCAGCAGCTCCTCTCGCGTAGGGGGCGCCTGAT
genomic: GACGAGAACCTCCCCATCATTGTCATTGCGACCCGCGACGCGTGCTTCAGgtaatgataa ... cctcttgcagCAAGCAGCAGTCGGTGATCCAACAGCTCCTCTCGCGCAGGGGGCGCCTGAT

EST: gi|89248870|gb|DY620656.1|DY620656

EST:     GACGAGAACCTCCCCATCATTGTCATTGCGACCCGCGACGCGTGCTTCAG                         CAAGCAGCAGTCGGTGATCCAACAGCTCCTCTCGCGCAGGGGGCGCCTGAT
genomic: GACGAGAACCTCCCCATCATTGTCATTGCGACCCGCGACGCGTGCTTCAGgtaatgataa ... cctcttgcagCAAGCAGCAGTCGGTGATCCAACAGCTCCTCTCGCGCAGGGGGCGCCTGAT

EST: gi|211507111|gb|FK960925.1|FK960925

EST:     GACGAGAACCTCCCCATCATTGTCATTGCGACTCGCGACGCGTGCTTCAG                         CAAGCAGCAGTCGGTGATCCAGCAGCTCCTCTCGCGTAGGGGGCG
genomic: GACGAGAACCTCCCCATCATTGTCATTGCGACCCGCGACGCGTGCTTCAGgtaatgataa ... cctcttgcagCAAGCAGCAGTCGGTGATCCAACAGCTCCTCTCGCGCAGGGGGCG

EST: gi|148955139|gb|EC900656.2|EC900656

EST:     GACGAGAACCTCCCCATCATTGTCATTGCGACCCGCGACGCGTGCTTCAG                         CAAGCAGCAGTCGGTGATCCAACAGCTCCTCTCGCGCAGGGGGCGCCTGAT
genomic: GACGAGAACCTCCCCATCATTGTCATTGCGACCCGCGACGCGTGCTTCAGgtaatgataa ... cctcttgcagCAAGCAGCAGTCGGTGATCCAACAGCTCCTCTCGCGCAGGGGGCGCCTGAT

EST: gi|71771453|gb|DR969390.1|DR969390

EST:     GACGAGAACCTCCCCATCATTGTCATTGCGACCCGCGACGCGTGCTTCAG                         CAAGCAGCAGTCGGTGATCCAACAGCTCCTCTCGCGCAGGGGGCGCCTGAT
genomic: GACGAGAACCTCCCCATCATTGTCATTGCGACCCGCGACGCGTGCTTCAGgtaatgataa ... cctcttgcagCAAGCAGCAGTCGGTGATCCAACAGCTCCTCTCGCGCAGGGGGCGCCTGAT

EST: gi|149005283|gb|EE039832.2|EE039832

EST:     GACGAGAACCTCCCCATCATTGTCATTGCGACCCGCGACGCGTGCTTCAG                         CAAGCAGCAGTCGGTGATCCAACAGCTCCTCTCGCGCAGGGGGCGCCTGAT
genomic: GACGAGAACCTCCCCATCATTGTCATTGCGACCCGCGACGCGTGCTTCAGgtaatgataa ... cctcttgcagCAAGCAGCAGTCGGTGATCCAACAGCTCCTCTCGCGCAGGGGGCGCCTGAT

EST: gi|47962136|gb|CN844845.1|CN844845

EST:     GACGAGAACCTCCCCATCATTGTCATTGCGACTCGCGACGCGTGCTTCAG                         CAAGCAGCAGTCGGTGATCCAGCAGCTCCTCTC
genomic: GACGAGAACCTCCCCATCATTGTCATTGCGACCCGCGACGCGTGCTTCAGgtaatgataa ... cctcttgcagCAAGCAGCAGTCGGTGATCCAACAGCTCCTCTC

EST: gi|211029256|gb|FL478423.1|FL478423

EST:     GACGAGAACCTCCCCATCATTGTCATTGCGACTCGCGACGCGTGCTTCAG                         CAAGCAGCAGTCGGTGATCCAGCAGCTCCTCTCGCGTAGGGGGCGCCTGAT
genomic: GACGAGAACCTCCCCATCATTGTCATTGCGACCCGCGACGCGTGCTTCAGgtaatgataa ... cctcttgcagCAAGCAGCAGTCGGTGATCCAACAGCTCCTCTCGCGCAGGGGGCGCCTGAT

EST: gi|149014771|gb|EE044463.2|EE044463

EST:     GACGAGAACCTCCCCATCATTGTCATTGCGACCCGCGACGCGTGCTTCAG                         CAAGCAGCAGTCGGTGATCCAACAGCTCCTCTCGCGCAGGGGGCGCCTGAT
genomic: GACGAGAACCTCCCCATCATTGTCATTGCGACCCGCGACGCGTGCTTCAGgtaatgataa ... cctcttgcagCAAGCAGCAGTCGGTGATCCAACAGCTCCTCTCGCGCAGGGGGCGCCTGAT

EST: gi|111197488|gb|EE295623.1|EE295623

EST:     CCGAGAACCTCCCCCATCATTGTCATTGCGACCCGCGACGCGTGCTTCAG                         CAAGCAGCAGTCGGTGATCCAACAGCTCCTCTCGCGCAGGGGGCGCCTGAT
genomic: ACGAGAACCT-CCCCATCATTGTCATTGCGACCCGCGACGCGTGCTTCAGgtaatgataa ... cctcttgcagCAAGCAGCAGTCGGTGATCCAACAGCTCCTCTCGCGCAGGGGGCGCCTGAT

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: 57

GCGAGGGCATGCTCGCTGGCGAGATGAAGCACGGGCCGCTGGCCCTCGTGGACGAGAACCTCCCCATCATTGTCATTGCGACCCGCGACGCGTGCTTCAGgtaatgataa ... cctcttgcagCAAGCAGCAGTCGGTGATCCAACAGCTCCTCTCGCGCAGGGGGCGCCTGATAGTGATGTGCTCTAGGGGAGATGCCGCGGCTGTGTGCCCTAGCGGTGGG

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 68

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 100