ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

ATATTAAAGGCTTTTTAAGTGATGTTAAACCAGCACTTCTAAGTGCCCTGGATACTGAATATGAGAAAAATCCTTTTGAGgtatgctgtgttacagtcactgtttggaaaatgcttacttattgcgactttgtttttcatcaacatctgtttggttcaattattag

Basic information

species	Zea mays
transcript	GRMZM2G009849_T03
intron #	6
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G009849_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os01g60040.2 (Oryza sativa), 5'ss of exon 24

ATATTAAAGGCTTTTTAAGTGATGTTAAACCAGCACTTCTAAGTGCCCTGGATACTGAATATGAGAAAAATCCTTTTGAGgtatgctgtgttacagtcactgtttggaaaatgcttacttattgcgactttgtttttcatcaacatctgtttggttcaattattag
|||| ||||||||  |||||||||| |||||||| ||||| ||| | |||||| ||||||||||||||||||| |||||||| || | | |  | | || ||||||||||||   | ||  || ||| |||  ||||||   |||||  ||| |||||||||  ||
ATATCAAAGGCTTCCTAAGTGATGTCAAACCAGCGCTTCTCAGTACTCTGGATGCTGAATATGAGAAAAATCCATTTGAGgtttgttctat--ctggcattgtttggaaaataagt-ctatttacgagttt--ttttcactgacatcaattttgttcaattaacag

upper sequence: GRMZM2G009849_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA20G32430.2 (Glycine max), 5'ss of exon 24

ATATTAAAGGCTTTTTAAGTGATGTTAAACCAGCACTTCTAAGTGCCCTGGATACTGAATATGAGAAAAATCCTTTTGAGgtatgctgtgttaca----gtcactgtttggaaaatgcttacttattgcgactttgtttttcatcaacatctgtttggttcaattattag----------
| |||||||| ||| | | |||||| ||||| ||||| || |||||||||||||| || |||||||| ||||| ||||||||||| | ||||  |    || | |  |  | |     |||  || ||           |  | |  |  | |     |        |            
ACATTAAAGGGTTTCTTACTGATGTAAAACCTGCACTGCTCAGTGCCCTGGATACGGAGTATGAGAAGAATCCATTTGAGgtatgttatgtttgatgaggttagttctatgcagggttttaaatagtggtgtagcagagtggagcggctccggcccactatgggggcttctgtagcggag

upper sequence: GRMZM2G009849_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA10G35140.1 (Glycine max), 5'ss of exon 26

--------------------ATATTAAAGGCTTTTTAAGTGATGTTAAACCAGCACTTCTAAGTGCCCTGGATACTGAATATGAGAAAAATCCTTTTGAGgtatgctgtgtt-----acagtcactgtttggaaaatgcttact----tattgcgactttgtttttcatca-----acatctgtttggttcaattattag
                    | |||||||| ||| | | |||||| || || ||||| || |||||||||||||| || |||||||| ||||| ||||||||||| | ||||     |   |   | | || |   |  | | |    |  |    |  |||     | ||     ||  |||   | | |      |  
TAAGGTTTTTCTCCTTGCAGACATTAAAGGGTTTCTTACTGATGTAAAGCCTGCACTGCTCAGTGCCCTGGATACAGAGTATGAGAAGAATCCATTTGAGgtatgttatgtttgatgaggtttgttctatgcagggttttaaatagcatgctatagcagtgtagcagagcagagtgacccctgcccgctacgggggctgc

upper sequence: GRMZM2G009849_T01 (Zea mays), 5'ss of exon 6
lower sequence: AT2G35630.1 (Arabidopsis thaliana), 5'ss of exon 24

ATATTAAAGGCTTTTTAAGTGATGTTAAACCAGCACTTCTAAGTGCCCTGGATACTGAATATGAGAAAAATCCTTTTGAGgtatgctgtgttacagtcactgtttggaaaatgcttacttattgcgactttgtttttcatcaacatctgtttggttcaattattag
| |||||||| ||| | | |||||| ||||| ||||| |||||||| || || || |||||||||||||| ||||| ||||||          ||||   ||| ||||      | | || |   |   ||||||||| |     |   | |  |    | || ||
ACATTAAAGGGTTTCTTAATGATGTCAAACCTGCACTACTAAGTGCACTTGACACCGAATATGAGAAAAACCCTTTCGAGgta----------cagt---tgtgtggattgccttgatttgtctagttcttgtttttc-ttgctgtacttatattatgttcatcag

upper sequence: GRMZM2G009849_T01 (Zea mays), 5'ss of exon 6
lower sequence: EFJ15655 (Selaginella moellendorffii), 5'ss of exon 23

ATATTAAAGGCTTTTTAAGTGATGTTAAACCAGCACTTCTAAGTGCCCTGGATACTGAATATGAGAAAAATCCTTTTGAGgtatgctgtgttacagtcactgtttggaaaatgcttacttattgcgactttgtttttcatcaacatctgtttggttcaattattag
   | ||    ||||| |  ||||| ||||| || |||| ||||||  ||||||| ||||||||||||||||| | |||||||        |||||  ||  ||    |  |  | | | ||  ||    |||||                               
GCTTGAAGAATTTTTTGACGGATGTGAAACCTGCTCTTCAAAGTGCTTTGGATACCGAATATGAGAAAAATCCCTATGAGgtag-------tacag--acccttcacgatttcttcattgatgtcgtaaatgtttcag----------------------------

upper sequence: GRMZM2G009849_T01 (Zea mays), 5'ss of exon 6
lower sequence: EFJ11209 (Selaginella moellendorffii), 5'ss of exon 23

ATATTAAAGGCTTTTTAAGTGATGTTAAACCAGCACTTCTAAGTGCCCTGGATACTGAATATGAGAAAAATCCTTTTGAGgtatgctgtgttacagtcactgtttggaaaatgcttacttattgcgactttgtttttcatcaacatctgtttggttcaattattag
   | ||    ||||| |  ||||| ||||| || |||| ||||||  ||||||| ||||||||||||||||| | |||||||        |||||  ||  ||    |  |  | | |  |  ||    |||||                               
GCTTGAAGAATTTTTTGACGGATGTGAAACCTGCTCTTCAAAGTGCTTTGGATACCGAATATGAGAAAAATCCCTATGAGgtag-------tacag--acccttcacgatttcttcattggtgtcgtaaatgtttcag----------------------------

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|19350672|gb|BM895204.1|BM895204

EST:     CAGCACTTCTAAGTGCCCTGGATACTGAATATGAGAAAAATCCTTTTGAG                         GGTGCTGCTGCTGCTCCAAAGAGAACAGTTCGAGTTCTGGATACTGCATCT
genomic: CAGCACTTCTAAGTGCCCTGGATACTGAATATGAGAAAAATCCTTTTGAGgtatgctgtg ... caattattagGGTGCTGCTGCTGCTCCAAAGAGAACAGTTCGAGTTCTGGATACTGCATCT

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: 108

ATATTAAAGGCTTTTTAAGTGATGTTAAACCAGCACTTCTAAGTGCCCTGGATACTGAATATGAGAAAAATCCTTTTGAGgtatgctgtg ... caattattagGGTGCTGCTGCTGCTCCAAAGAGAACAGTTCGAGTTCTGGATACTGCATCTTCTGTATCTGCCGGCTTGTCTGATGGGCTGCCACGGGAAGACATTAGTT

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 29

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 21