ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

TAATATAATAGAACCCTTCCATCGCTTCGTCGGATCAGAAATGATGACAGACCTCAGATACCCCATGAAGGGCAATACAGTGCCATTTTGGGCTGTGCCGgtaacatactgttctcttttggttttaccctgtcaatttcaatgaacctcttaaataagttttcttaatatcatgcttgttcag

Basic information

species	Zea mays
transcript	GRMZM2G077187_T01
intron #	2
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G077187_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os01g49820.1 (Oryza sativa), 5'ss of exon 2

TAATATAATAGAACCCTTCCATCGCTTCGTCGGATCAGAAATGATGACAGACCTCAGATACCCCATGAAGGGCAATACAGTGCCATTTTGGGCTGTGCCGgtaacatactgttctcttttggttttaccctgtcaatttcaatgaacctct-----taaataagttttcttaata--tcatgcttgttcag
 || ||||||||||| |||||||| || || ||||| || ||||||||||||||||||||||||||||| | ||| ||||| ||||||||||| || ||||||| | |   | | ||| | ||| || ||     |||||  |   ||| |     ||| |||  |||||| | |  ||||||||    ||
GAACATAATAGAACCATTCCATCGATTTGTTGGATCGGATATGATGACAGACCTCAGATACCCCATGAAAGACAACACAGTCCCATTTTGGGCGGTCCCGgtaa-acatcttacccttctagttctatccaacagatttcctttggcctgtacaggtaattaaagtttcttgaaaattcatgctttcgtag

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|76286378|gb|DV025946.1|DV025946

EST:     ACCTCAGATACCCCATGAAGGGCAATACAGTGCCATTTTGGGCTGTGCCG                         ATAATTGGTATCATTGGGCCTATGGTTATCATAACAGTGATATACTTTAAG
genomic: ACCTCAGATACCCCATGAAGGGCAATACAGTGCCATTTTGGGCTGTGCCGgtaacatact ... gcttgttcagATAATTGGTATCATTGGGCCTATGGTTATCATAACAGTGATATACTTTAAG

EST: gi|14243380|gb|BG841070.2|BG841070

EST:     ACCTCAGATACCCCATGAAGGGCAATACAGTGCCATTTTGGGCTGTGCCG                         ATAATTGGTATCATTGGGCCTATGGTTATCATAACAGTGATATACTTTAAG
genomic: ACCTCAGATACCCCATGAAGGGCAATACAGTGCCATTTTGGGCTGTGCCGgtaacatact ... gcttgttcagATAATTGGTATCATTGGGCCTATGGTTATCATAACAGTGATATACTTTAAG

EST: gi|76935224|gb|DV174245.1|DV174245

EST:     ACCTCAGATACCCCATGAAGGGCAATACAGTGCCATTTTGGGCTGTGCCG                         ATAATTGGTATCATTGGGCCTATGGTTATCATAACA
genomic: ACCTCAGATACCCCATGAAGGGCAATACAGTGCCATTTTGGGCTGTGCCGgtaacatact ... gcttgttcagATAATTGGTATCATTGGGCCTATGGTTATCATAACA

EST: gi|61119018|gb|DN559979.1|DN559979

EST:     ACCTCAGATACCCCATGAAGGGCAACACAGTGCCATTTTGGGCTGTGCCG                         ATAATTGGTATCATTGGGCCTATGGTTATCATAACAGTGATATACTTTAAG
genomic: ACCTCAGATACCCCATGAAGGGCAATACAGTGCCATTTTGGGCTGTGCCGgtaacatact ... gcttgttcagATAATTGGTATCATTGGGCCTATGGTTATCATAACAGTGATATACTTTAAG

EST: gi|78079032|gb|DV507444.1|DV507444

EST:     ACCTCAGATACCCCATGAAGGGCAATACAGTGCCATTTTGGGCTGTGCCG                         ATAATTGGTATCATTGGGCCTATGGTTATCATAACAGTGATATACTTTAAG
genomic: ACCTCAGATACCCCATGAAGGGCAATACAGTGCCATTTTGGGCTGTGCCGgtaacatact ... gcttgttcagATAATTGGTATCATTGGGCCTATGGTTATCATAACAGTGATATACTTTAAG

EST: gi|86467943|gb|DY234313.1|DY234313

EST:     ACCTCAGATACCCCATGAAGGGCAATACAGTGCCATTTTGGGCTGTGCCG                         ATAATTGGTATCATTGGGCCTATGGTTATCATAACAGTGATATACTTTAAG
genomic: ACCTCAGATACCCCATGAAGGGCAATACAGTGCCATTTTGGGCTGTGCCGgtaacatact ... gcttgttcagATAATTGGTATCATTGGGCCTATGGTTATCATAACAGTGATATACTTTAAG

EST: gi|76289091|gb|DV028659.1|DV028659

EST:     ACCTCAGATACCCCATGAAGGGCAATACAGTGCCATTTTGGGCTGTGCCG                         ATAATTGGTATCATTGGGCCTATGGTTATCATAACAGTGATATACTTTAAG
genomic: ACCTCAGATACCCCATGAAGGGCAATACAGTGCCATTTTGGGCTGTGCCGgtaacatact ... gcttgttcagATAATTGGTATCATTGGGCCTATGGTTATCATAACAGTGATATACTTTAAG

EST: gi|24934529|gb|CA452747.1|CA452747

EST:     ACCTCACTTACCCCATGAAGGGCAATACAGTGCCATTTTGGGCTGTGCCG                         ATAATTGGTATCATTGGGCCTATGGTTATCATAACAGTGATATACTTTAAG
genomic: ACCTCAGATACCCCATGAAGGGCAATACAGTGCCATTTTGGGCTGTGCCGgtaacatact ... gcttgttcagATAATTGGTATCATTGGGCCTATGGTTATCATAACAGTGATATACTTTAAG

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), 25 (downstream exon)
Score: 9

TAATATAATAGAACCCTTCCATCGCTTCGTCGGATCAGAAATGATGACAGACCTCAGATACCCCATGAAGGGCAATACAGTGCCATTTTGGGCTGTGCCGgtaacatact ... gcttgttcagATAATTGGTATCATTGGGCCTATGGTTATCATAACAGTGATATACTTTAAGAAGAGAAATGTATATGATCTGCATCATGCCATACTAG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 299

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 341