ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

TCTGTCTGAACTTAGTGGAGGACAACGATCCCTTCTTGCTCTTAGTCTTATCCTGGCTCTGCTTCTTTTTAAACCTGCACCACTTTACATATTGGACGAGgtatctctttaatatgatttactattcaaattccttaccactgcaatctactatttttgaactagtatgactttgctgtatttggaagaatgaggcggcg...

Basic information

species	Zea mays
transcript	GRMZM2G006452_T02
intron #	12
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G006452_T01 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os01g67740.1 (Oryza sativa), 5'ss of exon 18

TCTGTCTGAACTTAGTGGAGGACAACGATCCCTTCTTGCTCTTAGTCTTATCCTGGCTCTGCTTCTTTTTAAACCTGCACCACTTTACATATTGGACGAGgtatctctttaatatgatttactattcaaattcctta--ccactgcaatctact--atttttgaactagtatgactttgctgtatt-tggaagaatgaggcggcg
| | ||||||||||||||||| ||||| ||||| || |||||||||||||||||||| || |||||||| ||||||||||||||||| ||||| || ||||||| | |  |   |  |  |     ||  | || |   |||||  ||||||     |  ||| | || | ||  || | | | |  |   ||  | |||     
TTTATCTGAACTTAGTGGAGGGCAACGGTCCCTCCTCGCTCTTAGTCTTATCCTGGCGCTACTTCTTTTCAAACCTGCACCACTTTATATATTAGATGAGgtatgtttgcatcctattacaactaccagttaccatcatccactctaatctatctggtcattggaatactgtgtgttagttttgtaataagagcttcagg-----

upper sequence: GRMZM2G006452_T01 (Zea mays), 5'ss of exon 12
lower sequence: GLYMA12G36520.1 (Glycine max), 5'ss of exon 19

TCTGTCTGAACTTAGTGGAGGACAACGATCCCTTCTTGCTCTTAGTCTTATCCTGGCTCTGCTTCTTTTTAAACCTGCACCACTTTACATATTGGACGAGgtatctctttaatatgatttactattcaaattcctta---ccactgcaatctactatttttgaactagt---atgactttgctgtatttggaagaatgaggcggcg
  |||||||| | |||||||| || ||||| || ||||| |||  ||| || ||||| |||||||| || |||||||| |||||||||||  | || ||||||| | ||  | || | || || |  |  ||  |||    | | | ||   |  |    |||| || |   || |  |   | |   |  |   ||||  |    
ATTGTCTGAATTAAGTGGAGGTCAGCGATCACTGCTTGCACTTTCTCTGATTCTGGCACTGCTTCTGTTCAAACCTGCTCCACTTTACATCCTTGATGAGgtatgtttt--acattagtttctttgtattttttttagaatcccagtaaaacagaagcagtgaaatactgaaatcatctaagtttgccttaattcatgacac----

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|211018645|gb|FL458046.1|FL458046

EST:     CCACTTTACATATTGGACGAG                         GTTGATGCTGCTCTTGATCTGAGCCACACTCAAAACATT
genomic: CCACTTTACATATTGGACGAGgtatctcttt ... tgctctgcagGTTGATGCTGCTCTTGATCTGAGCCACACTCAAAACATT

EST: gi|60343263|gb|DN210236.1|DN210236

EST:     TCCTGGCTCTGCTTCTTTTTAAACCTGCACCACTTTACATATTGGACGAG                         GTTGATGCTGCTCTTGATCTGAGCCACACTCAAAACATTGGTAGAATGATC
genomic: TCCTGGCTCTGCTTCTTTTTAAACCTGCACCACTTTACATATTGGACGAGgtatctcttt ... tgctctgcagGTTGATGCTGCTCTTGATCTGAGCCACACTCAAAACATTGGTAGAATGATC

EST: gi|211376362|gb|FL264047.1|FL264047

EST:     CCACTTTACATATTGGACGAG                         GTTGATGCTGCTCTTGATCTGAGCCACACTCAAAACATTGGTAGAATGATC
genomic: CCACTTTACATATTGGACGAGgtatctcttt ... tgctctgcagGTTGATGCTGCTCTTGATCTGAGCCACACTCAAAACATTGGTAGAATGATC

EST: gi|22473074|gb|BU037554.1|BU037554

EST:     TCCTGGCTCTGCTTCTTTTTAAACCTGCACCACTTTACATATTGGACGAG                         GTTGATGCTGCTCTTGATCTGAGCCACACTCAAAACATTGGTAGAATGATC
genomic: TCCTGGCTCTGCTTCTTTTTAAACCTGCACCACTTTACATATTGGACGAGgtatctcttt ... tgctctgcagGTTGATGCTGCTCTTGATCTGAGCCACACTCAAAACATTGGTAGAATGATC

EST: gi|60342521|gb|DN209494.1|DN209494

EST:     TCCTGGCTCTGCTTCTTTTTAAACCTGCACCACTTTACATATTGGACGAG                         GTTGATGCTGCTCTTGATCTGAGCCACACTCAAAACATTGGTAGAATGATC
genomic: TCCTGGCTCTGCTTCTTTTTAAACCTGCACCACTTTACATATTGGACGAGgtatctcttt ... tgctctgcagGTTGATGCTGCTCTTGATCTGAGCCACACTCAAAACATTGGTAGAATGATC

EST: gi|6031321|gb|AW076178.1|AW076178

EST:     TCCTGGCTCTGCTTCTTTTTAAACCTGCACCACTTTACATATTGGACGAG                         GTTGATGCTGCTCTTGATCTGAGCCACACTCAAAACATTGGTAGAATGATC
genomic: TCCTGGCTCTGCTTCTTTTTAAACCTGCACCACTTTACATATTGGACGAGgtatctcttt ... tgctctgcagGTTGATGCTGCTCTTGATCTGAGCCACACTCAAAACATTGGTAGAATGATC

EST: gi|26457122|gb|CA828705.1|CA828705

EST:     TCCTGGCTCTGCTTCTTTTTAAACCTGCACCACTTTACATATTGGACGAG                         GTTGATGCTGCTCTTGATCTGAGCCACACTCAAAACATTGGTAGAATGATC
genomic: TCCTGGCTCTGCTTCTTTTTAAACCTGCACCACTTTACATATTGGACGAGgtatctcttt ... tgctctgcagGTTGATGCTGCTCTTGATCTGAGCCACACTCAAAACATTGGTAGAATGATC

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: 143

TCTGTCTGAACTTAGTGGAGGACAACGATCCCTTCTTGCTCTTAGTCTTATCCTGGCTCTGCTTCTTTTTAAACCTGCACCACTTTACATATTGGACGAGgtatctcttt ... tgctctgcagGTTGATGCTGCTCTTGATCTGAGCCACACTCAAAACATTGGTAGAATGATCAAGGCTCATTTTCCGCACTCTCAG

Block sizes: 46 (upstream exon), 46 (downstream exon)
Score: 36

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 51