ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GCTCGTCGTGGTGGAGTTGATGAGCCGTTTGCATGGGAAAGCAGAGAGTTTCTGAGGAAGCTCTGCATAGGGAAGgtgctacatttgaacttcatatcttctccgagctctcatatcattcattgtattcttttttttttgacactgcaaaattataatctcctgttaacag

Basic information

species	Zea mays
transcript	GRMZM2G136296_T01
intron #	3
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G136296_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os02g32350.2 (Oryza sativa), 5'ss of exon 3

GCTCGTCGTGGTGGAGTTGATGAGCCGTTTGCATGGGAAAGCAGAGAGTTTCTGAGGAAGCTCTGCATAGGGAAGgtgctacatttgaacttcatatcttctccgagctctcatatcattcattg-tattcttttttttttgacactgcaaaattataatctcctgttaacag-----------------------
||||| ||||||||||| ||||| || ||||| ||||||||||| |||||||| ||||| ||||||||||| ||||| || ||| |||| || | |||||||  ||  |  | ||  || ||| | |||   || | |||  | |   ||      |  |  ||||||| ||                        
GCTCGCCGTGGTGGAGTGGATGAACCATTTGCTTGGGAAAGCAGGGAGTTTCTAAGGAAACTCTGCATAGGAAAGgtactccatgtgaattttagatcttctttgaatttacttaa-atgcatagatatcgattgtgtttgtagaaaacatgccagt--ttccctgttaccaatgaaaaattcaaacatgttacag

upper sequence: GRMZM2G136296_T02 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA04G38010.1 (Glycine max), 5'ss of exon 3

GCTCGTCGTGGTGGAGTTGATGAGCCGTTTGCATGGGAAAGCAGAGAGTTTCTGAGGAAGCTCTGCATAGGGAAGgtgct---acatttgaact-----tcatatcttctccgagctctca----tatcattcattg--tattcttttttttttgacactgcaaaattat--aatctcctgttaacag-------------------------------
|| ||| | ||||| || || ||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||    | | ||||| |     ||||   ||     || |   |    ||  | |  |||  | ||  |||| | |||   |||   ||   |  ||| |     | |                                  
GCGCGTAGAGGTGGTGTGGACGAGCCTTTTGCATGGGAAAGCAGAGAGTTTCTGAGGAAGCTCTGCATAGGGAAGgtgcgttgaaaattgaaatagagttcattggttgattcagttgctactactactactacttgagtgttggttttgtcttgtttctggtgaagcgtgcaatttgtctctgatgtgatgggtatgttggaaatttttttggaacag

upper sequence: GRMZM2G136296_T02 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA05G33320.1 (Glycine max), 5'ss of exon 3

GCTCGTCGTGGTGGAGTTGATGAGCCGTTTGCATGGGAAAGCAGAGAGTTTCTGAGGAAGCTCTGCATAGGGAAGgtgctacatttgaacttcatatcttctccg------agctctcatatcattcattgtattcttttttttttga------cactgcaaaattataatctcctgt-taacag------
|| ||| | ||||| || ||||||||||||||||||||||| |||||||||||  ||||||||||||| ||||||||     |  |||  ||  | | ||| |        |||||| |      |  |    || | ||||||||        || |  ||   | | | ||  | | | |  |      
GCGCGTAGAGGTGGTGTAGATGAGCCGTTTGCATGGGAAAGTAGAGAGTTTCTACGGAAGCTCTGCATTGGGAAGgtaggcaaaatgatattttttttttcccgttttagtagctcttactctggtagtctgcttgtgttttttttagataaatcattctaagtctctgacctggtatatgattggaacag

upper sequence: GRMZM2G136296_T02 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA08G00910.1 (Glycine max), 5'ss of exon 3

GCTCGTCGTGGTGGAGTTGATGAGCCGTTTGCATGGGAAAGCAGAGAGTTTCTGAGGAAGCTCTGCATAGGGAAGgtgctacatttgaacttcatatcttctccgagctctcatatcattcatt-gtattcttttttttttgacactgcaaaatt-----ataatctcctgttaacag-------------------------------------
|| ||| | ||||| || |||||||||||||| |||||||| |||||||||||  ||||||| ||||| ||||||||     |  || | ||  | | |  ||    || |  |  |  | | | || |    |  |  || | | |  || |||      || | |  | || |                                        
GCGCGTAGAGGTGGTGTAGATGAGCCGTTTGCGTGGGAAAGTAGAGAGTTTCTACGGAAGCTTTGCATTGGGAAGgtaggcaaactgtattttttttttggtc---actttagttgcgcttactcgtgtgaagtaatcattaaaagtaaaatatttatcagtattttttttttcatttttttcaaagcctctgacctggtatatgattggaacag

upper sequence: GRMZM2G136296_T02 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA06G17050.4 (Glycine max), 5'ss of exon 3

GCTCGTCGTGGTGGAGTTGATGAGCCGTTTGCATGGGAAAGCAGAGAGTTTCTGAGGAAGCTCTGCATAGGGAAGgtgct---acatttgaacttcatatcttctccgagctctcatatcattcattgtattcttttttt--tttgac--actgcaaaattataatctcctgttaacag--------------------------------------------------------------
|| ||| | ||||| || || ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||    | | ||||| |  |  || |        ||   |   | |  |  ||    |  |||  | |||   | ||      | |  |||  | ||                                                                   
GCGCGTAGAGGTGGTGTGGACGAGCCGTTTGCATGGGAAAGCAGAGAGTTTCTGAGGAAGCTCTGCATAGGGAAGgtgcgttgaaaattgaaatagagttcattgattgattcagttgctactactactaccactactttgatctgatcgagtgtggtggttttgtcttgttttggtgaaagcgtgcaatgtgtctctgatgtgatggttttgttgggattttattttttttttggaacag

upper sequence: GRMZM2G136296_T02 (Zea mays), 5'ss of exon 3
lower sequence: AT5G07350.2 (Arabidopsis thaliana), 5'ss of exon 3

GCTCGTCGTGGTGGAGTTGATGAGCCGTTTGCATGGGAAAGCAGAGAGTTTCTGAGGAAGCTCTGCATAGGGAAGgtgctacatttgaacttcatatcttctccgagctctcatatcattcattgt-attcttttttttttgacactgcaaaattataatctcctgttaacag
|||||  | || ||  | |||||||| |||||||||||||||| ||| ||| ||||||| || |||||||| ||||||| | | |  || || ||| |   || |   |   | |  |   ||||| | |   | | ||||  ||   |||  || || |   | |       
GCTCGCAGAGGAGGTATAGATGAGCCTTTTGCATGGGAAAGCAAAGAATTTTTGAGGAAACTTTGCATAGGAAAGgtgc-aaagtcaaaattaataac---tcagttattatacactagctattgtgagtgactatattttctcatctcaagtttttatttgacag-------

upper sequence: GRMZM2G136296_T02 (Zea mays), 5'ss of exon 3
lower sequence: AT5G61780.1 (Arabidopsis thaliana), 5'ss of exon 3

GCTCGTCGTGGTGGAGTTGATGAGCCGTTTGCATGGGAAAGCAGAGAGTTTCTGAGGAAGCTCTGCATAGGGAAGgtgctacatttgaacttcatatcttctccgagctctcatatcattcattgta---ttcttttttttttgacactgcaaaattataatctcctgttaacag
|||||  | || ||  | |||||||| ||||||||||||||||| |||||||| |||||||| ||||| || ||||||||   ||| ||||   ||||   |  | | | | |  |     |||| |   || | ||  | || ||| |  |||  | |  | |    | | |||
GCTCGCAGAGGAGGTATAGATGAGCCTTTTGCATGGGAAAGCAGGGAGTTTCTAAGGAAGCTTTGCATTGGAAAGgtgctttgtttaaactctttatcacttatgtgttataagttatggaattgaaaagttttcttcatattaacagtttaaaccttttttttttcttgagcag

upper sequence: GRMZM2G136296_T02 (Zea mays), 5'ss of exon 3
lower sequence: Vv00s0283g00020.t01 (Vitis vinifera), 5'ss of exon 3

GCTCGTCGTGGTGGAGTTGATGAGCCGTTTGCATGGGAAAGCAGAGAGTTTCTGAGGAAGCTCTGCATAGGGAAGgtgct-acatttga-acttcatatcttctccgagctctcatatcattcattgtattcttttttttttgacactgcaaaattataatctcctgttaacag
|| ||| | ||||||||||||||||||||||||||||| |||||||||| | | |||||||||||||| || |||||||  | | || | |  |      || |    ||| | ||| |||||  | |         | ||  |   | |  ||| |||||   || | || ||
GCCCGTAGGGGTGGAGTTGATGAGCCGTTTGCATGGGACAGCAGAGAGTATTTAAGGAAGCTCTGCATTGGAAAGgtgcccatagttaacatgtttcggttttttttggctat-ataacattctcttttaagacagatgttgcatcttactcaat-ataat--tctttaaatag

upper sequence: GRMZM2G136296_T02 (Zea mays), 5'ss of exon 3
lower sequence: Vv14s0068g00720.t01 (Vitis vinifera), 5'ss of exon 2

GCTCGTCGTGGTGGAGTTGATGAGCCGTTTGCATGGGAAAGCAGAGAGTTTCTGAGGAAGCTCTGCATAGGGAAGgtgctac--atttgaacttcatatcttctccga--gctctcatatcattcattgtattcttttttttttgacactgcaaaattataatctcctgt-taacag
|| ||| | |||||  ||||||| || ||||||||||| || ||||||| | ||||||| ||||||||||| |||||||  |  ||   |  ||  |  ||| |  |      || ||||  |   ||| |   |   |  | |   |||   |  || |  | |    |  || ||
GCCCGTAGAGGTGGTATTGATGAACCATTTGCATGGGATAGTAGAGAGTATTTGAGGAAACTCTGCATAGGAAAGgtgcctctcatacaacttttcttccttttatggtgatcctaatattctcttttgaaccatgaatcctgtcttactcagatgttgttgtattgattacaatag

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|71441098|gb|DR822148.1|DR822148

EST:     CGTTTGCATGGGAAAGCAGAGAGTTTCTGAGGAAGCTCTGCATAGGGAAG                         GAGGTCACATTCAAAGTGGATTATACAGCTCCTAATATTGGACGAGAATTT
genomic: CGTTTGCATGGGAAAGCAGAGAGTTTCTGAGGAAGCTCTGCATAGGGAAGgtgctacatt ... ctgttaacagGAGGTCACATTCAAAGTGGATTATACAGCTCCTAATATTGGACGAGAATTT

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: 482

GCTCGTCGTGGTGGAGTTGATGAGCCGTTTGCATGGGAAAGCAGAGAGTTTCTGAGGAAGCTCTGCATAGGGAAGgtgctacatt ... ctgttaacagGAGGTCACATTCAAAGTGGATTATACAGCTCCTAATATTGGACGAGAATTTGGAACTGTTTTTCTATGTGATAAGAATGTTGCATACTCAGTAGTTTCTG

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 405

Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 568