ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

TTACAGTGGAAAGAACACTCTATGATATTCGCCATGCCAAACAAGCCAGGAGAATTCAGCCGGTTTGATTTCCCAGAAACTTTGCCAGCACCTATAAATGgtaagttatacacaacggtggagttattgcaacaggttctctcatttttgctaatatatggacattattaggggtttattagtgacaataataacattacatcgttaccgttgagcttaactctgctaattgatgtcatactgtgattcactattttgcttttaacag

Basic information

species	Zea mays
transcript	GRMZM2G410515_T01
intron #	6
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G410515_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os03g08570.1 (Oryza sativa), 5'ss of exon 6

TTACAGTGGAAAGAACACTCTATGATATTCGCCATGCCAAACAAGCCAGGAGAATTCAGCCGGTTTGATTTCCCAGAAACTTTGCCAGCACCTATAAATGgtaag-ttatacacaacggtggagttattgcaacaggttctctcatttttgctaatatatggacattattaggggtttattagtgacaataataacattacatcgttaccgttgagcttaactctgctaattgatgtcatactgtgattcactattttgcttttaacag
|| || ||||| |||||||| |||||||| ||||||||||||||||||||||||||||||||||||||||| || ||||| ||||| |||||  |||||||| || | |||  || || ||||||| ||  |  |    |    |||      | || || |    |||| | ||||  ||  |     || |||||    |  || |                                                             
TTGCAATGGAAGGAACACTCCATGATATTTGCCATGCCAAACAAGCCAGGAGAATTCAGCCGGTTTGATTTTCCTGAAACATTGCCTGCACCCTTAAATGgtgagatcatatgcagcgctggagttgtttaattaaa--ccaagattcccagaagtacatcg----tattggtggttactt--ttgttttactaacacatgactgtaa-------------------------------------------------------------

upper sequence: GRMZM2G410515_T01 (Zea mays), 5'ss of exon 6
lower sequence: Vv09s0002g00100.t01 (Vitis vinifera), 5'ss of exon 6

TTACAGTGGAAAGAACACTCTATGATATTCGCCATGCCAAACAAGCCAGGAGAATTCAGCCGGTTTGATTTCCCAGAAACTTTGCCAGCACCTATAAATGgtaagttatacacaacggtggagttattgcaacaggttctctcatttttgctaat-atatggacattattaggggtttattagtgacaataataacattacatcgttaccgttgagcttaactctgctaattgatgtcatactgtgattcactattttgcttttaacag
|| |||||||| ||||| ||||||||||| || | ||||| ||||||||| ||||||||||| ||||||||||| |||    | || |||||  |||||||| ||  |  || ||   |  | |      |      |||  ||| ||||   || ||  | ||| | | |    | | ||| ||| ||    |   | ||                                                                    
TTGCAGTGGAAGGAACATTCTATGATATTTGCAAAGCCAAGCAAGCCAGGGGAATTCAGCCGATTTGATTTCCCTGAAGTCCTTCCTGCACCCTTAAATGgtgagcaactcataagcatc-attagcaatatttaagtcttgcatctttgtatatgatgagcacaatttaatttttcttttaatgaaaaattcagtgtgac--------------------------------------------------------------------

upper sequence: GRMZM2G410515_T01 (Zea mays), 5'ss of exon 6
lower sequence: PP1S369_27V6.1 (Physcomitrella patens), 5'ss of exon 4

---TTACAGTGGAAAGAACACTCTATGATATTCGCCATGCCAAACAAGCCAGGAGAATTCAGCCGGTTTGATTTCCCAGAAACTTTGCCAGCACCTATAAATGgtaagttatacacaacggtggagttattgcaacaggttctctcatttttgctaatatatggacattattaggggtttattagtgacaataataacattacatcgttaccgttgagcttaactctgctaattgatgtcatactgtgattcactattttgcttttaacag
    | |||||||| || |||   ||||| || || ||||| ||||| || ||||| |||||||| ||||||||||||||||   | || |||||| | ||||||||||      |    || || ||       |  |  | |   |     |||  |  | ||| || ||    ||  |   ||  ||| |||    | | ||  |||  |||  |  |||       |||   || |||  |                          
CGTCTTCAGTGGAAGGAGCACAGCATGATCTTTGCAATGCCCAACAAACCTGGAGAGTTCAGCCGCTTTGATTTCCCAGAAA---TCCCTGCACCTCTCAATGgtaagtgtccatcttttgtagattt-------cgagaccccgtctgcgcactagaagtttgactttgttttatgtgcag-ggtcccaaaaattggctcagat-attagtgttttgaataatgtaagcaat--gtggcatgtttcag----------------------

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|71765383|gb|DR963320.1|DR963320

EST:     AGAATTCAGCCGGTTTGATTTCCCAGAAACTTTGCCAGCACCTATAAATG                         GGATATGGGGCATATTGAGAAACAATGAAATGCTT
genomic: AGAATTCAGCCGGTTTGATTTCCCAGAAACTTTGCCAGCACCTATAAATGgtaagttata ... cttttaacagGGATATGGGCCATATTGAGAAACAATGAAATGCTT

EST: gi|211323424|gb|FL039624.1|FL039624

EST:     AGAATTCAGCCGGTTTGATTTCCCAGAAACTTTGCCAGCACCTATAAATG                         GGATATGGGCCATATTGAGAAACAATGAAATGCTTACTTGGCCGGAGAAGG
genomic: AGAATTCAGCCGGTTTGATTTCCCAGAAACTTTGCCAGCACCTATAAATGgtaagttata ... cttttaacagGGATATGGGCCATATTGAGAAACAATGAAATGCTTACCTGGCCCGAGAAGG

EST: gi|76294009|gb|DV033577.1|DV033577

EST:     AGAATTCAGCCGGGTTGATTTCCCAGAAACTTTGCCAGCACCTATAAATG                         GGATATGGGCCATATTGAGAAACAATGAAATGCTTACCTGG
genomic: AGAATTCAGCCGGTTTGATTTCCCAGAAACTTTGCCAGCACCTATAAATGgtaagttata ... cttttaacagGGATATGGGCCATATTGAGAAACAATGAAATGCTTACCTGG

EST: gi|78075888|gb|DV504322.1|DV504322

EST:     AGAATTCAGCCGGTTTGATTTCCCAGAAACTTTGCCAGCACCTATAAATG                         GGATATGGGCCATATTGAGAAACAATGAAATGCTTACCTGGCCCGA
genomic: AGAATTCAGCCGGTTTGATTTCCCAGAAACTTTGCCAGCACCTATAAATGgtaagttata ... cttttaacagGGATATGGGCCATATTGAGAAACAATGAAATGCTTACCTGGCCCGA

EST: gi|211417850|gb|FL018180.1|FL018180

EST:     AGAATTCAGCCGGTTTGATTTCCCAGAAACTTTGC-AGCACCTATAAATG                         GGATATGG-CCATATTGA
genomic: AGAATTCAGCCGGTTTGATTTCCCAGAAACTTTGCCAGCACCTATAAATGgtaagttata ... cttttaacagGGATATGGGCCATATTGA

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: 48 (upstream exon), 44 (downstream exon)
Score: 47

TTACAGTGGAAAGAACACTCTATGATATTCGCCATGCCAAACAAGCCAGGAGAATTCAGCCGGTTTGATTTCCCAGAAACTTTGCCAGCACCTATAAATGgtaagttata ... cttttaacagGGATATGGGCCATATTGAGAAACAATGAAATGCTTACCTGGCCCGAGAAGGTGAAGTTTGCAATCGGACTTCTGCCAGCAATGGTTGGTGGTCAACCTTA

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 167

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 84