ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

TGATACCTGGTTCCGCCGATGGTCTGTATGAGTTTGGTTCGTTCATGTCAGCCACACTGAGCTGTGACCACAGGGTTATAGATGgtaagctattggtctttgtgcgatgcctccatggactgtggactgggaattaactatgctgttcatggaaactgtgcag

Basic information

species	Zea mays
transcript	GRMZM2G161969_T01
intron #	14
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G161969_T01 (Zea mays), 5'ss of exon 14
lower sequence: LOC_Os02g01500.1 (Oryza sativa), 5'ss of exon 18

------------TGATACCTGGTTCCGCCGATGGTCTGTATGAGTTTGGTTCGTTCATGTCAGCCACACTGAGCTGTGACCACAGGGTTATAGATGgtaagctattggtctttgt--------gcgatgcctccatggactgtggactgggaattaactatgctgttcatggaaactgtgcag
            ||||||||||   ||  || || | ||||||||||||||| |||||||| || ||| |||||||||| ||||||||||| |||||||  || ||   | || |          |||   || | ||||  | | || | || ||||| || |  |  ||     | |  ||
CTGAGAAGAGGGTGATACCTGGCAGCGTAGACGGCCAGTATGAGTTTGGTTCCTTCATGTCGGCAACAATGAGCTGTGATCACAGGGTTATTGATGgtatactcttaagccttatctgaatacatgatagttctacggaccataggctagaaaataactttgttcat-gtgtgctttctctag

upper sequence: GRMZM2G161969_T01 (Zea mays), 5'ss of exon 14
lower sequence: LOC_Os07g22720.2 (Oryza sativa), 5'ss of exon 18

------------TGATACCTGGTTCCGCCGATGGTCTGTATGAGTTTGGTTCGTTCATGTCAGCCACACTGAGCTGTGACCACAGGGTTATAGATGgtaagctatt--ggtctt-------tgtgcgatgcctccatggactgtggactgggaattaactatgctgttcatggaaactgtgcag
            ||||||||||   |||| ||||||  || ||||||||||| |||||||| || ||| |||||||||| ||||||||||| |||||||  || ||  | ||||       |    |||| || ||||||   ||| |  | |||||||| |  |  |  ||       |  ||
CTGAGAGGAGGGTGATACCTGGCAGCGCCAATGGTCAATACGAGTTTGGTTCCTTCATGTCGGCAACAATGAGCTGTGATCACAGGGTTATTGATGgtatactctttagatcttatcggaataaatgatggcttcatggatcatgggcaagaaattaacttttgttcttgtgcgcttactctag

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|20301579|gb|BQ164522.1|BQ164522

EST:     TGGTTCGTTCATGTCAGCCACACTGAGCTGTGACCACAGGGTTATAGATG                         GTGCAATCGGTGCGGAATTTCTGAAAGCATTCAAGGGCTACATCGAGAACC
genomic: TGGTTCGTTCATGTCAGCCACACTGAGCTGTGACCACAGGGTTATAGATGgtaagctatt ... aactgtgcagGTGCAATCGGTGCGGAATTTCTGAAAGCATTCAAGGGCTACATCGAGAACC

EST: gi|20336914|gb|BQ172544.1|BQ172544

EST:     TGGTTCGTTCATGTCAGCCACACTGAGCTGTGACCACAGGGTTATAGATG                         GTGCAATCGGTGCGGAATTTCTGAGAGCATTCAAGGGCTACATCGAGAACC
genomic: TGGTTCGTTCATGTCAGCCACACTGAGCTGTGACCACAGGGTTATAGATGgtaagctatt ... aactgtgcagGTGCAATCGGTGCGGAATTTCTGAAAGCATTCAAGGGCTACATCGAGAACC

EST: gi|71329666|gb|DR801555.1|DR801555

EST:     TGGTTCGTTCATGTCAGCCACACTGAGCTGTGACCACAGGGTTATAGATG                         GTGCAATCGGTGCGGAATTTCTGAAAGCATTCAAGGGCTACATCGAGAACC
genomic: TGGTTCGTTCATGTCAGCCACACTGAGCTGTGACCACAGGGTTATAGATGgtaagctatt ... aactgtgcagGTGCAATCGGTGCGGAATTTCTGAAAGCATTCAAGGGCTACATCGAGAACC

EST: gi|21809699|gb|BQ668017.1|BQ668017

EST:     TGGTTCGTTCATGTCAGCCACACTGAGCTGTGACCACAGGGTTATAGATG                         GTGCAATCGGTGCGGAATTTCTGAAAGCATTCAAGGGCTACATCGAGAACC
genomic: TGGTTCGTTCATGTCAGCCACACTGAGCTGTGACCACAGGGTTATAGATGgtaagctatt ... aactgtgcagGTGCAATCGGTGCGGAATTTCTGAAAGCATTCAAGGGCTACATCGAGAACC

EST: gi|5439400|gb|AI820321.1|AI820321

EST:     TGGTTCGTTCATGTCAGCCACACTGAGCTGTGACCACAGGGTTATAGATG                         GTGCAATCGGTGCGGAATTTCTGAAAGCATTCAAGGGCTACATCGAGAACC
genomic: TGGTTCGTTCATGTCAGCCACACTGAGCTGTGACCACAGGGTTATAGATGgtaagctatt ... aactgtgcagGTGCAATCGGTGCGGAATTTCTGAAAGCATTCAAGGGCTACATCGAGAACC

EST: gi|20208397|gb|BQ134486.1|BQ134486

EST:     TGGTTCGTTCATGTCAGCCACACTGAGCTGTGACCACAGGGTTATAGATG                         GTGCAATCGGTGCGGAATTTCTGAAAGCATTCAAGGGCTACATCGAGAACC
genomic: TGGTTCGTTCATGTCAGCCACACTGAGCTGTGACCACAGGGTTATAGATGgtaagctatt ... aactgtgcagGTGCAATCGGTGCGGAATTTCTGAAAGCATTCAAGGGCTACATCGAGAACC

EST: gi|5343148|gb|AI795333.1|AI795333

EST:     TGGTTCGTTCATGTCAGCCACACTGAGCTGTGACCACAGGGTTATAGATG                         GTGCAATCGGTGCGGAATTTCTGAAAGCATTCAAGGGCTACATCGAGAACC
genomic: TGGTTCGTTCATGTCAGCCACACTGAGCTGTGACCACAGGGTTATAGATGgtaagctatt ... aactgtgcagGTGCAATCGGTGCGGAATTTCTGAAAGCATTCAAGGGCTACATCGAGAACC

EST: gi|148935652|gb|EC879696.2|EC879696

EST:     TGGTTCGTTCATGTCAGCCACACTGAGCTGTGACCACAGGGTTATAGATG                         GTGCAATCGGTGCGGAATTTCTGAAAGCATTCAAGGGCTACATCGAGAACC
genomic: TGGTTCGTTCATGTCAGCCACACTGAGCTGTGACCACAGGGTTATAGATGgtaagctatt ... aactgtgcagGTGCAATCGGTGCGGAATTTCTGAAAGCATTCAAGGGCTACATCGAGAACC

EST: gi|4776441|gb|AI665444.1|AI665444

EST:     TGGTTCGTTCATGTCAGCCACACTGAGCTGTGACCACAGGGTTATAGATG                         GTGCAATCGGTGCGGAATTTCTGAAAGCATTCAAGGGCTACATCGAGAACC
genomic: TGGTTCGTTCATGTCAGCCACACTGAGCTGTGACCACAGGGTTATAGATGgtaagctatt ... aactgtgcagGTGCAATCGGTGCGGAATTTCTGAAAGCATTCAAGGGCTACATCGAGAACC

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: 112

TGATACCTGGTTCCGCCGATGGTCTGTATGAGTTTGGTTCGTTCATGTCAGCCACACTGAGCTGTGACCACAGGGTTATAGATGgtaagctatt ... aactgtgcagGTGCAATCGGTGCGGAATTTCTGAAAGCATTCAAGGGCTACATCGAGAACCCGACTTCGATGCTGCTGTGAAGTTAGGATCGATGACCTAACACAATTCT

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 105

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 108