ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

ATGTTGGAACTATTAGAATTCAGCGACCGCATAAAGGACCCTTCTATGTATCACCAAAAAGCATCGATCAACTTATTATGAATCTTGGAAAATGGGCCAAgtaggaaaaattgttagaacttagaacattttcttttgttcttagttagggtatcttatgctagtagcatgtttgtgacag

Basic information

species	Zea mays
transcript	GRMZM5G871572_T01
intron #	7
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM5G871572_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os07g45350.3 (Oryza sativa), 5'ss of exon 7

ATGTTGGAACTATTAGAATTCAGCGACCGCATAAAGGACCCTTCTATGTATCACCAAAAAGCATCGATCAACTTATTATGAATCTTGGAAAATGGGCCAAgtaggaaaaattgttagaacttagaacattttcttttgttcttagttagggtatcttatgctagtagcatgttt-gtgacag---
|||||||||||||| ||||||||||||| || |||||||| || |||||||| || |||||||||||||||||||| ||||||||||| |||||||||||||| ||| |  ||        ||||| ||| ||| |  ||     ||||| |   | | |||| |||  |||||    |||    
ATGTTGGAACTATTCGAATTCAGCGACCACACAAAGGACCATTTTATGTATCCCCGAAAAGCATCGATCAACTTATCATGAATCTTGGGAAATGGGCCAAgtatgaaga--tgcag-----tagaatattctctctcttt-----ttaggcttcttgaggctaatagtgtgttttactacaacag

upper sequence: GRMZM5G871572_T01 (Zea mays), 5'ss of exon 7
lower sequence: Vv07s0104g00630.t01 (Vitis vinifera), 5'ss of exon 7

ATGTTGGAACTATTAGAATTCAGCGACCGCATAAAGGACCCTTCTATGTATCACCAAAAAGCATCGATCAACTTATTATGAATCTTGGAAAATGGGCCAAgt-------aggaaaaattgttagaacttaga----acattttcttttgttcttagttagggtatcttatgctagtagcatgtttgtga-cag
|||||||||| ||| | |||||||| || ||||||||||| || ||||| || || ||||| || ||||| ||| ||   |||||||| |||||||| | ||       | || || || ||      ||||    | ||  |  ||| |  ||  ||    |  ||| | ||   |     |||||   |||
ATGTTGGAACAATTCGTATTCAGCGGCCCCATAAAGGACCATTTTATGTCTCTCCCAAAAGTATTGATCATCTTGTTGCAAATCTTGGCAAATGGGCAAGgttgtacataagataactttttttttgatagaccgcatatgatactttttcttttctttcttttccttttccttaca-tgcatttgtcctcag

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|91054019|gb|EB164437.1|EB164437

EST:     AAAAAGCATCGATCAACTTATTATGAATCTTGGAAAATGGGCCAA                         GTTATACCGCCTTGCTTCAATGGGCTTTGCAACATTTGGTGCCTTCCTTCT
genomic: AAAAAGCATCGATCAACTTATTATGAATCTTGGAAAATGGGCCAAgtaggaaaaa ... tttgtgacagGTTATACCGCCTTGCTTCAATGGGCTTTGCAACATTTGGTGCCTTCCTTCT

EST: gi|211009140|gb|FL186793.1|FL186793

EST:     TCACCAAAAAGCATCGATCAACTTATTATGAATCTTGGAAAATGGGCCAA                         GTTATACCGCCTTGCTTCAATGGGCTTTGCAACATTTGGTGCC-TCCTTCT
genomic: TCACCAAAAAGCATCGATCAACTTATTATGAATCTTGGAAAATGGGCCAAgtaggaaaaa ... tttgtgacagGTTATACCGCCTTGCTTCAATGGGCTTTGCAACATTTGGTGCCTTCCTTCT

EST: gi|56691676|gb|CX129579.1|CX129579

EST:     TCACCAAAAAGCATCGATCAACTTATTATGAATCTTGGAAAATGGGCCAA                         GTTATACCGCCTTGCTTCAATGGGCTTTGCAACATTTGGCGCCTTCCTTCT
genomic: TCACCAAAAAGCATCGATCAACTTATTATGAATCTTGGAAAATGGGCCAAgtaggaaaaa ... tttgtgacagGTTATACCGCCTTGCTTCAATGGGCTTTGCAACATTTGGTGCCTTCCTTCT

EST: gi|78114654|gb|DV533042.1|DV533042

EST:     AAATGGGCCAA                         GTTATACCGCCTTGCTTCAATGGGCTTTGCAACATTTGGTGCCTTCCTTCT
genomic: AAATGGGCCAAgtaggaaaaa ... tttgtgacagGTTATACCGCCTTGCTTCAATGGGCTTTGCAACATTTGGTGCCTTCCTTCT

EST: gi|149055712|gb|EE156420.2|EE156420

EST:     TCACCAAAAAGCATCGATCAACTTATTATGAATCTTGGAAAATGGGCCAA                         GTTATACCGCCTTGCTTCAATGG
genomic: TCACCAAAAAGCATCGATCAACTTATTATGAATCTTGGAAAATGGGCCAAgtaggaaaaa ... tttgtgacagGTTATACCGCCTTGCTTCAATGG

EST: gi|71432571|gb|DR813621.1|DR813621

EST:     TCACCAAAAAGCATCGATCAACTTATTATGAATCTTGGAAAATGGGCCAA                         GTTATACCGCCTTGCTTCAATGGGCTTTGCAACATTTGGTGCCTTCCTTTC
genomic: TCACCAAAAAGCATCGATCAACTTATTATGAATCTTGGAAAATGGGCCAAgtaggaaaaa ... tttgtgacagGTTATACCGCCTTGCTTCAATGGGCTTTGCAACATTTGGTGCCTTCCTT-C

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), 47 (downstream exon)
Score: 130

ATGTTGGAACTATTAGAATTCAGCGACCGCATAAAGGACCCTTCTATGTATCACCAAAAAGCATCGATCAACTTATTATGAATCTTGGAAAATGGGCCAAgtaggaaaaa ... tttgtgacagGTTATACCGCCTTGCTTCAATGGGCTTTGCAACATTTGGTGCCTTCCTTCTTGCAAAGCGTGCAATACAACATTTTCTAGAAAGAAAGCGCCGGCATGAA

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 96

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 114