ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GAAATTCACTTGCATGGTAATGGGATTGGGAATGAGGGAATACGTGAGTTGATGTCTGCATTATCTGCTCACAAAGgtgccttttttcctggctaaagaaactatcaagcctatgcttattggattttattcctaattatgcgcgtgcttggctgaattacag

Basic information

species	Zea mays
transcript	GRMZM2G110289_T01
intron #	9
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G110289_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os06g13050.1 (Oryza sativa), 5'ss of exon 10

GAAATTCACTTGCATGGTAATGGGATTGGGAATGAGGGAATACGTGAGTTGATGTCTGCATTATCTGCTCACAAAGgtgccttttttcctggctaaagaaactatcaagcctatgcttattggatt--ttattcctaattatgcgcgtgcttggctgaattacag
||| |||| |||||||| |||||  |||||||||||||| ||||||  |||||||| || || |||||||||||||||     |||||    ||||| |||  | | ||    | ||||  |||||  ||   ||  ||| || || | ||||| |||| |||||
GAACTTCATTTGCATGGCAATGGTTTTGGGAATGAGGGAGTACGTGCATTGATGTCAGCGTTGTCTGCTCACAAAGgta----ttttctgcactaaacaaatcaactagtagcttcttacgggattagtttacccctattttg-gccttcttggatgaactacag

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|15208880|gb|BI430764.1|BI430764

EST:     GGGAATGAGGGAATACGTGAGTTGATGTCTGCATTATCTGCTCACAAAG                         GGAAGATCACAGTTGTGGATATTGGCAACAACAACATTAGCCCGGAAGGTT
genomic: GGGAATGAGGGAATACGTGAGTTGATGTCTGCATTATCTGCTCACAAAGgtgccttttt ... tgaattacagGGAAGATCACAGTTGTGGATATTGGCAACAACAACATTAGCCCGGAAGGTT

EST: gi|18384682|gb|BM417881.1|BM417881

EST:     TGGGAATGAGGGAATACGTGAGTTGATGTCTGCATTATCTGCTCACAAAG                         GGAAGATCACAGTTGTGGATATTGGCAACAACAACATTAGCCCGGAAGGTT
genomic: TGGGAATGAGGGAATACGTGAGTTGATGTCTGCATTATCTGCTCACAAAGgtgccttttt ... tgaattacagGGAAGATCACAGTTGTGGATATTGGCAACAACAACATTAGCCCGGAAGGTT

EST: gi|18384842|gb|BM418041.1|BM418041

EST:     TGGGAATCAGGGAATACGTGAGTTGATGTCTGCATTATCTGCTCACAAAG                         GGAAGATCACAGTTGTGGATATTGGCAACAACAACATTAGCCCGGAAGGTT
genomic: TGGGAATGAGGGAATACGTGAGTTGATGTCTGCATTATCTGCTCACAAAGgtgccttttt ... tgaattacagGGAAGATCACAGTTGTGGATATTGGCAACAACAACATTAGCCCGGAAGGTT

EST: gi|67010636|gb|CO439385.1|CO439385

EST:     ATGAGGGAATACGTGAGTTGATGTCTGCATTATCTGCTCACAAAGG                         GGAAGATCACAGTTGTGGATATTGGCAACAACAACATTAGCCCGGAAGGT
genomic: ATGAGGGAATACGTGAGTTGATGTCTGCATTATCTGCTCACAAA-Ggtgccttttt ... tgaattacagGGAAGATCACAGTTGTGGATATTGGCAACAACAACATTAGCCCGGAAGGT

EST: gi|18384843|gb|BM418042.1|BM418042

EST:     TGGGAATGAGGGAATACGTGAGTTGATGTCTGCATTATCTGCTCACAAAG                         GGAAGATCACAGTTGTGGATATTGGCAACAACAACATTAGCCCGGAAGGTT
genomic: TGGGAATGAGGGAATACGTGAGTTGATGTCTGCATTATCTGCTCACAAAGgtgccttttt ... tgaattacagGGAAGATCACAGTTGTGGATATTGGCAACAACAACATTAGCCCGGAAGGTT

EST: gi|16746087|gb|BM032517.1|BM032517

EST:     TGGGAATGAGGGAATACGTGAGTTGATGTCTGCATTATCTGCTCACAAAG                         GGAAGATCACAGTTGTGGATATTGGCAACAACAACATTAGCCCGGAAGGTT
genomic: TGGGAATGAGGGAATACGTGAGTTGATGTCTGCATTATCTGCTCACAAAGgtgccttttt ... tgaattacagGGAAGATCACAGTTGTGGATATTGGCAACAACAACATTAGCCCGGAAGGTT

EST: gi|18384841|gb|BM418040.1|BM418040

EST:     TGGGAATGAGGGAATACGTGAGTTGATGTCTGCATTATCTGCTCACAAAG                         GGAAGATCACAGTTGTGGATATTGGCAACAACAACATTAGCCCGGAAGGTT
genomic: TGGGAATGAGGGAATACGTGAGTTGATGTCTGCATTATCTGCTCACAAAGgtgccttttt ... tgaattacagGGAAGATCACAGTTGTGGATATTGGCAACAACAACATTAGCCCGGAAGGTT

EST: gi|12046108|gb|BF728247.1|BF728247

EST:     TGGGAATGAGGGAATACGTGAGTTGATGTCTGCATTATCTGCTCACAAAG                         GGAAGATCACAGTTGTGGATATTGGCAACAACAACATTAGCCCGGATGGTT
genomic: TGGGAATGAGGGAATACGTGAGTTGATGTCTGCATTATCTGCTCACAAAGgtgccttttt ... tgaattacagGGAAGATCACAGTTGTGGATATTGGCAACAACAACATTAGCCCGGAAGGTT

EST: gi|18384685|gb|BM417884.1|BM417884

EST:     TGGGAATGAGGGAATACGTGAGTTGATGTCTGCATTATCTGCTCACAAAG                         GGAAGATCACAGTTGTGGATATTGGCAACAACAACATTAGCCCGGAAGGTT
genomic: TGGGAATGAGGGAATACGTGAGTTGATGTCTGCATTATCTGCTCACAAAGgtgccttttt ... tgaattacagGGAAGATCACAGTTGTGGATATTGGCAACAACAACATTAGCCCGGAAGGTT

EST: gi|18384683|gb|BM417882.1|BM417882

EST:     TGGGAATGAGGGAATACGTGAGTTGATGTCTGCATTATCTGCTCACAAAG                         GGAAGATCACAGTTGTGGATATTGGCAACAACAACATTAGCCCGGAAGGTT
genomic: TGGGAATGAGGGAATACGTGAGTTGATGTCTGCATTATCTGCTCACAAAGgtgccttttt ... tgaattacagGGAAGATCACAGTTGTGGATATTGGCAACAACAACATTAGCCCGGAAGGTT

EST: gi|16745974|gb|BM032404.1|BM032404

EST:     TGGGAATGAGGGAATACGTGAGTTGATGTCTGCATTATCTGCTCACAAAG                         GGAAGATCACAGTTGTGGATATTGGC
genomic: TGGGAATGAGGGAATACGTGAGTTGATGTCTGCATTATCTGCTCACAAAGgtgccttttt ... tgaattacagGGAAGATCACAGTTGTGGATATTGGC

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: 45 (upstream exon), 49 (downstream exon)
Score: 75

GAAATTCACTTGCATGGTAATGGGATTGGGAATGAGGGAATACGTGAGTTGATGTCTGCATTATCTGCTCACAAAGgtgccttttt ... tgaattacagGGAAGATCACAGTTGTGGATATTGGCAACAACAACATTAGCCCGGAAGGTTTACATCCTGTAGCCGAGTTCCTCAAAAGGACAAAGTCCTTACAGTGGTT

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 197

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 98