ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

CTAATTCTAAGCCCTGTCCAAAGTGCAAACGGCCAATAGAGAAAAACCAGGGATGCATGCATATGACATGCACCCCTCCTTGTAAATTCGAATTTTGCTGgtattgttcacttactgcttgaaagaattgcagtattctgccatgtttatcttcttttgtcttgaggttctttgcacattccag

Basic information

species	Zea mays
transcript	GRMZM2G100913_T02
intron #	8
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G100913_T02 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os08g42740.2 (Oryza sativa), 5'ss of exon 8

CTAATTCTAAGCCCTGTCCAAAGTGCAAACGGCCAATAGAGAAAAACCAGGGATGCATGCATATGACATGCACCCCTCCTTGTAAATTCGAATTTTGCTGgtattgttcact-----tactgcttgaaagaattgcagtattctgccatgtttatcttcttttgtcttgaggttctttgcacattccag
||||||||||||| || ||||| |||||||| ||||||||||||||||||||||||||||||||||| ||||| || ||||| ||||| || || ||||||||| || || |     | ||   ||||| | ||       | |  |  || ||| | | | |   |||   ||||||| ||||| |||
CTAATTCTAAGCCGTGCCCAAAATGCAAACGACCAATAGAGAAAAACCAGGGATGCATGCATATGACTTGCACTCCACCTTGCAAATTTGAGTTCTGCTGgtatagtccaatgtctatgcttgctgaaatatttatgtccatattactagtgtatgtacctctcatttgtt-ttctttgaacatttcag

upper sequence: GRMZM2G100913_T02 (Zea mays), 5'ss of exon 8
lower sequence: AT1G65430.1 (Arabidopsis thaliana), 5'ss of exon 8

CTAATTCTAAGCCCTGTCCAAAGTGCAAACGGCCAATAGAGAAAAACCAGGGATGCATGCATATGACATGCACCCCTCCTTGTAAATTCGAATTTTGCTGgta---ttgttcacttactgcttgaaagaattgcagtattctgccatgtttatcttcttttgtcttgaggttctttgcacattccag--------------
| ||||| |||||||||||||| ||||||||||||||||||||||||||||| || |||||||| || |||||||| || |||||||| || || ||||||||   |  |  | |   || || ||  || |||  || | |   | |||   ||| | || |||  |   |   || | ||   |               
CAAATTCCAAGCCCTGTCCAAAATGCAAACGGCCAATAGAGAAAAACCAGGGTTGTATGCATATTACGTGCACCCCACCATGTAAATTTGAGTTCTGCTGgtaagttgataaagtggttgattaaacaaaatgctataatgtcagaagttatgcttttattctctctatacttcctgta-atctaactctgaattggattc

upper sequence: GRMZM2G100913_T02 (Zea mays), 5'ss of exon 8
lower sequence: PP1S114_2V6.1 (Physcomitrella patens), 5'ss of exon 8

CTAATTCTAAGCCCTGTCCAAAGTGCAAACGGCCAATAGAGAAAAACCAGGGATGCATGCATATGACATGCACCCCTCCTTGTAAATTCGAATTTTGCTGgta--ttgttcacttactgcttgaaagaattgcagt--attctgccat------gtttatcttcttttgtcttgaggttc---tttgcacattccag------------------------------------------------------------------------------------------------------
| ||    || || || || ||||| ||  ||||||| ||||||||||| || ||||||||||| || ||||| || ||||| |||   || |||||||||||     || | |      || ||| ||| |   |  ||| | || |      ||| | ||| ||      |||  |||    |||| ||||                                                                                                          
CAAACAGCAAACCTTGCCCCAAGTGTAAGAGGCCAATTGAGAAAAACCAAGGCTGCATGCATATCACTTGCACTCCACCTTGCAAACATGAGTTTTGCTGgtaaacaatttaatgtaattttaaaaaaatagttttttattttcccttattgaagttaagcttgttaacgaatgaaattcggtcttgctcattaagctcatcagtgcagctgcggcagtccatgctattgtattttaacgctttgagtgtctggtttggaaatagtgtcacttacaagagttcactgatactataacag

upper sequence: GRMZM2G100913_T02 (Zea mays), 5'ss of exon 8
lower sequence: PP1S156_28V6.1 (Physcomitrella patens), 5'ss of exon 8

CTAATTCTAAGCCCTGTCCAAAGTGCAAACGGCCAATAGAGAAAAACCAGGGATGCATGCATATGACATGCACCCCTCCTTGTAAATTCGAATTTTGCTGgta-------------ttgttca--cttactgcttgaaagaattgcagtattctgccatgtttatcttcttttgtcttgaggttctttgcacatt--ccag-----------------------------------------------------------------
| ||    || ||||| || || || ||| ||||||| ||||||||||| || || ||||| || || ||||| |||||||| ||||| || |||||||||||             || ||    ||    |  |||| |  ||  | |   ||  |    | |||     | ||  | | ||| ||    | ||  || |                                                                 
CAAACAGCAAACCCTGCCCCAAATGTAAAAGGCCAATTGAGAAAAACCAAGGGTGTATGCACATTACTTGCACACCTCCTTGCAAATTTGAGTTTTGCTGgtaagtctaatagattttattgggtctcgaggaatgaatgggtttaaattcactctccaactcatcgataatggttcttaagtttttgttgctttagcctgaatgggttgaaagctggtcattgataagacacttacttatgagcaacccacttttgtttctaaag

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|87156257|gb|DY401046.1|DY401046

EST:     GGATGCATGCATATGACATGCACCCCTCCTTGTAAATTCGAATTTTGCTG                         GTTATGTCTGGGTGCATGGTCAGATCATGGAGAGAGAACAGGTGGCTTTTA
genomic: GGATGCATGCATATGACATGCACCCCTCCTTGTAAATTCGAATTTTGCTGgtattgttca ... cacattccagGTTATGTCTGGGTGCATGGTCAGATCACGGAGAGAGAACAGGTGGCTTTTA

EST: gi|26559055|gb|CA831290.1|CA831290

EST:     GGATGCATGCATATGACATGCACCCCTCCTTGTAAATTCGAATTTTGCTG                         GTTATGTCTGGGTGCATGGTCAGATCATGGAGAGAGAACAGGTGGCTTTTA
genomic: GGATGCATGCATATGACATGCACCCCTCCTTGTAAATTCGAATTTTGCTGgtattgttca ... cacattccagGTTATGTCTGGGTGCATGGTCAGATCACGGAGAGAGAACAGGTGGCTTTTA

EST: gi|31364271|gb|CD448626.1|CD448626

EST:     ATGACATGCACCCCTCCTTGTAAATTCGAATTTTGCTG                         GTTATGTCTGGGTGCATGGTCAGATCATGGAGAGAGAACAGGTGGCTTTTA
genomic: ATGACATGCACCCCTCCTTGTAAATTCGAATTTTGCTGgtattgttca ... cacattccagGTTATGTCTGGGTGCATGGTCAGATCACGGAGAGAGAACAGGTGGCTTTTA

EST: gi|213179909|gb|FM186344.1|FM186344

EST:     GGATGCATGCATATGACATGCACTCCTCCTTGTAAATTCGAATTTTGCTG                         GTTATGTCTGGGTGCATGGTCAGATCACGGAGAGAGAACAGGTGGCTTTTA
genomic: GGATGCATGCATATGACATGCACCCCTCCTTGTAAATTCGAATTTTGCTGgtattgttca ... cacattccagGTTATGTCTGGGTGCATGGTCAGATCACGGAGAGAGAACAGGTGGCTTTTA

EST: gi|22549188|gb|BU101389.1|BU101389

EST:     GGATGCATGCATATGACATGCACCCCTCCTTGTAAATTCGAATTTTGCTG                         GTTATGTCTGGGTGCATGGTCAGATCATGGAGAGAGAACAGGTGGCTTTTA
genomic: GGATGCATGCATATGACATGCACCCCTCCTTGTAAATTCGAATTTTGCTGgtattgttca ... cacattccagGTTATGTCTGGGTGCATGGTCAGATCACGGAGAGAGAACAGGTGGCTTTTA

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: 47 (upstream exon), 49 (downstream exon)
Score: 246

CTAATTCTAAGCCCTGTCCAAAGTGCAAACGGCCAATAGAGAAAAACCAGGGATGCATGCATATGACATGCACCCCTCCTTGTAAATTCGAATTTTGCTGgtattgttca ... cacattccagGTTATGTCTGGGTGCATGGTCAGATCACGGAGAGAGAACAGGTGGCTTTTATGCTTGCAATCGTTATGAATCAGCAAAGAAAGAGGGAGTT

Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 261

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 279