ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GCCATGCCAGTGTTTGACATGATAGAGACGGTGCTGGTGAAGAAGCTGCGCTTCCCTCCCGGTCTGACACTGCGTCTCATCTCTCGGACCGCCTATGTTGgtaatgaacgccccccgtcaaatctgaactgaacttgtacagccgaattggcgcctcactgaactaaggtgatgcaacctgtacgtatgtgcag

Basic information

species	Zea mays
transcript	GRMZM2G046743_T01
intron #	4
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G046743_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os08g03350.1 (Oryza sativa), 5'ss of exon 3

GCCATGCCAGTGTTTGACATGATAGAGACGGTGCTGGTGAAGAAGCTGCGCTTCCCTCCCGGTCTGACACTGCGTCTCATCTCTCGGACCGCCTATGTTGgtaatgaacgccccc-cgtcaa--atctgaactgaacttgtacagccgaattggcgcctcactgaactaaggtgatgcaacctgtacgtatgtgcag
|||||||| ||||| |||||||| ||||| ||||| || ||||||||  | ||||||||||| || || || || |||||| |  | ||   ||| ||||||||  |  |  |    ||  |  ||||||||| ||||           ||| |  | |  |    || |         | ||| |  | |||||||
GCCATGCCGGTGTTCGACATGATCGAGACCGTGCTCGTCAAGAAGCTCAGATTCCCTCCCGGCCTCACGCTTCGCCTCATCGCAAGAACACTCTACGTTGgtaagcactgttcaagtgttcatcatctgaacttaactgaatttttt--attagatcttggcatggctgaaac----tgatctgga-atctgtgcag

upper sequence: GRMZM2G046743_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA19G22590.1 (Glycine max), 5'ss of exon 5

GCCATGCCAGTGTTTGACATGATAGAGACGGTGCTGGTGAAGAAGCTGCGCTTCCCTCCCGGTCTGACACTGCGTCTCATCTCTCGGACCGCCTATGTTGgtaatgaacgccccccg--tcaaatctg--aactgaacttgtacagccgaattg-gcgcctcactgaactaagg-tgatgcaacctgtacg--tatgtgcag-------------------------------------
|| |||||||||||||||||||| || |||||| |||| |||||  ||   |||   ||  |    |  || ||| |  |    || |  |  ||||| |||||  ||| |   |     ||||||    ||   |||   |  |   |  ||   |   |   |     |    | ||| |     || |  |||||| |                                      
GCAATGCCAGTGTTTGACATGATTGAAACGGTGATGGTCAAGAAATTGAATTTCGAACCAAGCAGAATGCTTCGTTTTGTTGTACGTAATGTATATGTGGgtaagtaactctttctcatccaaatcaagtaatgcaaccaatgtacatgttttttacatgttgttatgtcacttctaatggatttcctatggttatgtgtattgatatatcctctctcttttttttctttttttttcag

upper sequence: GRMZM2G046743_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA16G06750.1 (Glycine max), 5'ss of exon 4

GCCATGCCAGTGTTTGACATGATAGAGACGGTGCTGGTGAAGAAGCTGCGCTTCCCTCCCGGTCTGACACTGCGTCTCATCTCTCGGACCGCCTATGTTGgtaatgaacgccccccgtcaaatctgaactgaacttgtacagccgaattggcgcctcactgaactaaggtgatgcaacctgtacgtatgtgcag-------------------------------------
|| |||||||||||||||||||| || || ||| ||||||||||  ||  |||    ||  || ||||||| ||| | ||    || |     ||||| ||||| | |  | |  ||| |    |||| || |  | |       |   |     |||||   |||| |   | ||     |     | ||                                        
GCAATGCCAGTGTTTGACATGATTGAAACTGTGATGGTGAAGAAATTGAACTTTAAACCTAGTATGACACTTCGTTTTATTGTACGCAATCTGTATGTGGgtaa-gtaaacacttcgtaatcattgaagtgtatgttttgtcataagcagatatttcactt--ctaatggatttcatttcattttggtttgtgactcagttcaattgatatattattctctttgttttcag

upper sequence: GRMZM2G046743_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA19G24520.1 (Glycine max), 5'ss of exon 4

GCCATGCCAGTGTTTGACATGATAGAGACGGTGCTGGTGAAGAAGCTGCGCTTCCCTCCCGGTCTGACACTGCGTCTCATCTCTCGGACCGCCTATGTTGgtaa-tgaacgccccccgtcaaatctgaactgaacttgtacagccgaattggcgcctcactgaactaaggt---gatgcaacctgtacgtatgtgcag---------------------------
|| |||||||||||||||||||| || || ||| ||||||||||| ||  ||||   ||  ||   ||||| ||| ||||    || | ||  ||||| ||||| | ||| |   |     | |      |   ||||  ||    |   |     ||| |  |   |  |     |      |||   |  |||||                            
GCAATGCCAGTGTTTGACATGATTGAAACTGTGATGGTGAAGAAGTTGAACTTCAAACCTAGTAGTACACTTCGTTTCATTGTACGCAACGTGTATGTGGgtaagtaaacactttctaattattaaagtatatgcttggtca--taagcagatatttcagttcatggatatttcattttggtttgtgactcagtgcaattaacatatcattctctttgttttcag

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|78092654|gb|DV521028.1|DV521028

EST:     CTTCCCTCCCGGTCTGACACTGCGTCTCATCTCTCGGACCGCCTATGTTG                         CGTTCACAATGTTCATCGCCATCACCTTCCCCTTCTTCGGCGGACTGCTCG
genomic: CTTCCCTCCCGGTCTGACACTGCGTCTCATCTCTCGGACCGCCTATGTTGgtaatgaacg ... gtatgtgcagCGTTCACAATGTTCATCGCCATCACCTTCCCCTTCTTCGGCGGACTGCTCG

EST: gi|71761350|gb|DR959287.1|DR959287

EST:     CTTCCCTCCCGGTCTGACACTGCGTCTCATCTCTCGGACCGCCTATGTTG                         CGTTCACAATGTTCATCGCCATCACCTTCCCCTTCTTCGGCGGACTGCTCG
genomic: CTTCCCTCCCGGTCTGACACTGCGTCTCATCTCTCGGACCGCCTATGTTGgtaatgaacg ... gtatgtgcagCGTTCACAATGTTCATCGCCATCACCTTCCCCTTCTTCGGCGGACTGCTCG

EST: gi|149000252|gb|EE037405.2|EE037405

EST:     CTTCCCTCCCGGTCTGACACTGCGTCTCATCTCTCGGACCGCCTATGTTG                         CGTTCACAATGTTCATCGCCATCACCTTCCCCTTCTTCGGCGGACTGCTCG
genomic: CTTCCCTCCCGGTCTGACACTGCGTCTCATCTCTCGGACCGCCTATGTTGgtaatgaacg ... gtatgtgcagCGTTCACAATGTTCATCGCCATCACCTTCCCCTTCTTCGGCGGACTGCTCG

EST: gi|37385478|gb|CF629883.1|CF629883

EST:     CTTCCCTCCCGGTCTGACACTGCGTCTCATCTCTCGGACCGCCTATGTTG                         CGTTCACAATGTTCATCGCCATCACCTTCCCCTTCTTCGGCGGACTGCTCG
genomic: CTTCCCTCCCGGTCTGACACTGCGTCTCATCTCTCGGACCGCCTATGTTGgtaatgaacg ... gtatgtgcagCGTTCACAATGTTCATCGCCATCACCTTCCCCTTCTTCGGCGGACTGCTCG

EST: gi|50336113|gb|CO531239.1|CO531239

EST:     CTTCCCTCCCGGTCTGACACTGCGTCTCATCTCTCGGACCGCCTATGTTG                         CGTTCACAATGTTCATCGCCATCACCTTCCCCTTCTTCGGCGGACTGCTCG
genomic: CTTCCCTCCCGGTCTGACACTGCGTCTCATCTCTCGGACCGCCTATGTTGgtaatgaacg ... gtatgtgcagCGTTCACAATGTTCATCGCCATCACCTTCCCCTTCTTCGGCGGACTGCTCG

EST: gi|40334334|gb|CK368404.1|CK368404

EST:     CTTCCCTCCCGGTCTGACACTGCGTCTCATCTCTCGGACCGCCTATGTTG                         CGTTCACAATGTTCATCGCCATCACCTTCCCCTTCTTCGGCGGACTGCTCG
genomic: CTTCCCTCCCGGTCTGACACTGCGTCTCATCTCTCGGACCGCCTATGTTGgtaatgaacg ... gtatgtgcagCGTTCACAATGTTCATCGCCATCACCTTCCCCTTCTTCGGCGGACTGCTCG

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 3 RNA-Seq libraries.

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 82

GCCATGCCAGTGTTTGACATGATAGAGACGGTGCTGGTGAAGAAGCTGCGCTTCCCTCCCGGTCTGACACTGCGTCTCATCTCTCGGACCGCCTATGTTGgtaatgaacg ... gtatgtgcagCGTTCACAATGTTCATCGCCATCACCTTCCCCTTCTTCGGCGGACTGCTCGGCTTCTTCGGCGGATTCGCCTTTGCACCGACGACCTATTTC

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 253