ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

CACGGGCATGTTGGGTTCATGATGTCATGCTATGATGCAGCGCTCAGTTACGATTTCCATACCGACACATTCCGTGCAAGgtatgttctgacgatttgtatggtggatacatacaaactgaaaaaacttgtttcttcaaattcttaaaactggtcatcatgtggcag

Basic information

species	Zea mays
transcript	GRMZM2G130348_T01
intron #	2
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G130348_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os01g17390.1 (Oryza sativa), 5'ss of exon 2

CACGGGCATGTTGGGTTCATGATGTCATGCTATGATGCAGCGCTCAGTTACGATTTCCATACCGACACATTCCGTGCAAGgtatgttctgacgatttgtatggtggatacatacaaactgaaaaaacttgtttcttcaaattcttaaaact----ggtcatcatgtggcag---------------------------------------------------------------------
|| ||||||||||| ||||||||||||||||| ||||||| |||||| || |||||||| |  || || ||||||||||||||    ||    | | || | |||  |  |       |  ||       | |  | |  | || |  | |    ||  | ||  | ||||                                                                     
CATGGGCATGTTGGATTCATGATGTCATGCTACGATGCAGAGCTCAGCTATGATTTCCACAGTGATACCTTCCGTGCAAGgtactaacttcttactggtttagtgattttagctgtggttgaatgtaaattgtggttatgtcctgatgattttgaggcgaacacatagcagcacaaagattttatatcctctgaagattgtatcttcaagttatctaactggccttaaaaacattgacag

upper sequence: GRMZM2G130348_T01 (Zea mays), 5'ss of exon 2
lower sequence: AT2G26850.1 (Arabidopsis thaliana), 5'ss of exon 2

CACGGGCATGTTGGGTTCATGATGTCATGCTATGATGCAGCGCTCAGTTACGATTTCCATACCGACACATTCCGTGCAAGgtatgttctgacg-atttgtatggtggatacatacaaactgaaaaaacttgtttcttcaaattcttaaaactggtcatcatgtggcag-----
 | || ||||| ||||||||| |||||||||||||||| | |||||| || ||     | ||  | || || |  || ||||||    |     || |  ||  |  | ||| | |   ||   |    |  ||| |  ||| ||  |||||   |   ||   | |      
AATGGACATGTAGGGTTCATGTTGTCATGCTATGATGCTGAGCTCAGCTATGACACTGACACTAATACTTTTCAAGCTAGgtataaaatatttcatgtccatattcaacaca-atattttgctta----ttcttcatagaatgctataaactatactgtattgaggattttag

upper sequence: GRMZM2G130348_T01 (Zea mays), 5'ss of exon 2
lower sequence: AT2G32560.1 (Arabidopsis thaliana), 5'ss of exon 2

CACGGGCATGTTGGGTTCATGATGTCATGCTATGATGCAGCGCTCAGTTACGATTTCCATACCGACACATTCCGTGCAAGgtatgttctgacgatttgtatggtggatacatacaaactgaaaaaacttgtttcttcaaattcttaaaactggtcatcatgtggcag-----
 | || ||||| ||||||||| |||||||||||||||| | |||||| || |||   || || || || ||||  || ||||||      |  || | ||  ||  | |  |  |  || | |||  || ||  |||  ||  |  ||  |     | ||  || ||     
AATGGACATGTAGGGTTCATGTTGTCATGCTATGATGCGGAGCTCAGCTATGATACTCACACGGATACGTTCCAAGCCAGgtat------aaaatatctaatgtccacatttg-acgctaacaaattttcttatttctcatcat--aagtttacgtttattggggagtttag

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|149000598|gb|EE037796.2|EE037796

EST:     TATGATGCAGCGCTCAGTTACGATTTCCATACCGACACATTCCGTGCAAG                         GTACCCACCACACGGTCGACGAACCGTGGTGTTGGAGGATGGCGTGCAATG
genomic: TATGATGCAGCGCTCAGTTACGATTTCCATACCGACACATTCCGTGCAAGgtatgttctg ... catgtggcagGTACCCACCACACGGTCGACGAACCGTGGTGTTGGAGGATGGCGTGCAATG

EST: gi|149009737|gb|EE154079.2|EE154079

EST:     TATGATGCAGCGCTCAGTTACGATTTCCATACCGACACATTCCGTGCAAG                         GTACCCACCACACGGTCGACGAACCGTGGTGTTGGAGGATGGCGTGCAATG
genomic: TATGATGCAGCGCTCAGTTACGATTTCCATACCGACACATTCCGTGCAAGgtatgttctg ... catgtggcagGTACCCACCACACGGTCGACGAACCGTGGTGTTGGAGGATGGCGTGCAATG

EST: gi|21330588|gb|BQ485969.1|BQ485969

EST:     ACGATTTCCATACCGACACATTCCGTGCAAG                         GTACCCACCACACGGTCGACGAACCGCGGTGCTGGAGGATGGCGTGCAATG
genomic: ACGATTTCCATACCGACACATTCCGTGCAAGgtatgttctg ... catgtggcagGTACCCACCACACGGTCGACGAACCGTGGTGTTGGAGGATGGCGTGCAATG

EST: gi|6012313|gb|AW061669.1|AW061669

EST:     GCAGCGCTCAGTTACGATTTGCATACCGACACATTCCGTGCAAG                         GTACCCACCACACGGTCGACGAACCGTGGTGTTGGAGGATGGCGTGCAATG
genomic: GCAGCGCTCAGTTACGATTTCCATACCGACACATTCCGTGCAAGgtatgttctg ... catgtggcagGTACCCACCACACGGTCGACGAACCGTGGTGTTGGAGGATGGCGTGCAATG

EST: gi|21331057|gb|BQ486438.1|BQ486438

EST:     TATGATGCAGCGCTCAGTTACGATTTCCATACCGACACATTCCGTGCAAG                         GTACCCACCACACGGTCGACGAACCGTGGTGTTGGAGGATGGCGTGCAATG
genomic: TATGATGCAGCGCTCAGTTACGATTTCCATACCGACACATTCCGTGCAAGgtatgttctg ... catgtggcagGTACCCACCACACGGTCGACGAACCGTGGTGTTGGAGGATGGCGTGCAATG

EST: gi|71771776|gb|DR969713.1|DR969713

EST:     TATGATGCAGCGCTCAGTTACGATTTCCATACCGACACATTCCGTGCAAG                         GTACCCACCACACGGTCGACGAACCGTGGTGTTGGAGGATGGCGTGCAATG
genomic: TATGATGCAGCGCTCAGTTACGATTTCCATACCGACACATTCCGTGCAAGgtatgttctg ... catgtggcagGTACCCACCACACGGTCGACGAACCGTGGTGTTGGAGGATGGCGTGCAATG

EST: gi|76013482|gb|DT940652.1|DT940652

EST:     TATGATGCAGCGCTCAGTTACGATTTCCATACCGACACATTCCGTGCAAG                         GTACCCACCACACGGTCGACGAACCGTGGTGTTGGAGGATGGCGTGCAATG
genomic: TATGATGCAGCGCTCAGTTACGATTTCCATACCGACACATTCCGTGCAAGgtatgttctg ... catgtggcagGTACCCACCACACGGTCGACGAACCGTGGTGTTGGAGGATGGCGTGCAATG

EST: gi|26455381|gb|CA826964.1|CA826964

EST:     TATGATGCAGCGCTCAGTTACGATTTCCATACCGACACATTCCGTGCAAG                         GTACCCACCACACGGTCGACGAACCGTGGTGTTGGAGGATGGCGTGCAATG
genomic: TATGATGCAGCGCTCAGTTACGATTTCCATACCGACACATTCCGTGCAAGgtatgttctg ... catgtggcagGTACCCACCACACGGTCGACGAACCGTGGTGTTGGAGGATGGCGTGCAATG

EST: gi|14203843|gb|BG837520.1|BG837520

EST:     TATGATGCAGCGCTCAGTTACGATTTCCATACCGACACATTCCGTGCAAR                         GTACCCACCACACGGTCGACGAACCGTGGTCTTGGAGGATGGCGTGCAATG
genomic: TATGATGCAGCGCTCAGTTACGATTTCCATACCGACACATTCCGTGCAAGgtatgttctg ... catgtggcagGTACCCACCACACGGTCGACGAACCGTGGTGTTGGAGGATGGCGTGCAATG

EST: gi|71771777|gb|DR969714.1|DR969714

EST:     TATGATGCAGCGCTCAGTTACGATTTCCATACCGACACATTCCGTGCAAG                         GTACCCACCACACGGTCGACGAACCGTGGTGTTGGAGGATGGCGTGCAATG
genomic: TATGATGCAGCGCTCAGTTACGATTTCCATACCGACACATTCCGTGCAAGgtatgttctg ... catgtggcagGTACCCACCACACGGTCGACGAACCGTGGTGTTGGAGGATGGCGTGCAATG

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: 102

CACGGGCATGTTGGGTTCATGATGTCATGCTATGATGCAGCGCTCAGTTACGATTTCCATACCGACACATTCCGTGCAAGgtatgttctg ... catgtggcagGTACCCACCACACGGTCGACGAACCGTGGTGTTGGAGGATGGCGTGCAATGGGACAGGGTGAGGGCACCGCCTGTTGACACCCTTGCGCATGACCTGCAC

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 91

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 91