ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GACTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTAAAGTTTCCAATTAGGCTTGAGGGCCTTGCCTATTCTCATGGTGCCTTCTCAAGTgtatgtccaatgattgcttattttggcatcacaattttttttacctttttttttgtctcccttcttggaatttgacatttttcatttgttttacag

Basic information

species	Zea mays
transcript	GRMZM2G149238_T04
intron #	6
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G149238_T04 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os03g45410.1 (Oryza sativa), 5'ss of exon 7

GACTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTAAAGTTTCCAATTAGGCTTGAGGGCCTTGCCTATTCTCATGGTGCCTTCTCAAGTgtatgtccaatgattgcttattttggcatcacaattttttttacctttttttttgtctcccttcttggaatttgacatttttcatttgttttacag
|| || ||||||||||| |||||||||||||||||||| || |||||||| ||||| ||||| ||||| |||||||||||||| |||||||||||| ||  | |  |||| |   ||    | |  |    ||| || ||| || | ||    ||| |     |        |||  | |   | ||||
GATTTCAAGATTCAGAACATTGTTGGCTCTTGTGATGTTAAATTTCCAATCAGGCTGGAGGGACTTGCATATTCTCATGGTGCTTTCTCAAGTgtaagttgagtccttgcatgccttt---ttaggacgcctttcacatttgttat-gttgttcttat----gtcctgtgccttttgtgt---taacag

upper sequence: GRMZM2G149238_T04 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os12g39070.1 (Oryza sativa), 5'ss of exon 6

GACTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTAAAGTTTCCAATTAGGCTTGAGGGCCTTGCCTATTCTCATGGTGCCTTCTCAAGTgtatgtccaatgattgcttattttggcatcacaattttttttacctttttttttgtctcccttcttggaatttgacatttttcatttgttttacag
||||| ||||||||||| |||||||| ||||||||||| || |||||||| ||||| ||||| ||||| |||||||||||||| |||||||||||| ||  |||  |||| | ||||   |  | | ||| ||| || | | || |     |  ||||      |||     |  | ||||| || |||
GACTTCAAGATTCAGAACATTGTTGGTTCTTGTGATGTTAAATTTCCAATCAGGCTGGAGGGACTTGCATATTCTCATGGTGCTTTCTCAAGTgtaagttgaatccttgcatgtttttttaggata-tttctttcacatatgttatg----ctattctcatgtcttg-----tgccttttgtcttccag

upper sequence: GRMZM2G149238_T04 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA18G44460.1 (Glycine max), 5'ss of exon 6

-GACTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTAAAGTTTCCAATTAGGCTTGAGGGCCTTGCCTATTCTCATGGTGCCTTCTCAAGTgtatgtccaatgattgcttattttggcatcacaattttttttacctttttttttgtctcccttcttggaatttgacatttt--tcatttgttttacag-------
 || ||||||||||||||||||||||||||||||||||||||||| || ||| | || ||||| ||||||||||| |||||||| |||||||||||| ||   |        | || |    |     | ||  |      ||| || |          |  || ||    |  |  | ||  ||  || |        
GGATTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTAAAGTTCCCCATTCGACTGGAGGGTCTTGCCTATTCCCATGGTGCTTTCTCAAGtgtaagtgtgaaa------tgttataatcttctgttcttcctggtgaatttcttggaaaaatggtctacaaattcctgtcctagttatcagtactatatatggtcc

upper sequence: GRMZM2G149238_T04 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA19G28780.1 (Glycine max), 5'ss of exon 7

GACTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTAAAGTTTCCAATTAGGCTTGAGGGCCTTGCCTATTCTCATGGTGCCTTCTCAAGTgtatgtc-------caatgattgcttattttggcatcacaatttttttta----cctttttttttgtctcccttcttggaatttgacatttttcatttgttttacag
|| |||||||||||||| |||||||||||||||||||| ||||| || ||| | |||||||| ||||||||||| ||| |||| |||||||||||| ||        |||| ||    | ||||  |     |||||  |  |       |  |       |||   | | | | |     |  |  || || |      
GATTTTAAGATTCAGAACATTGTTGGCTCTTGTGATGTCAAGTTCCCCATTCGACTTGAGGGTCTTGCCTATTCCCATAGTGCTTTCTCAAGTgtaagtgtgaaatgcaataatcatctgtttttcctggtgaatttcatggaaaaatggtcctcacaaattcctgccctagtaatcag--tcctatatatggtc-----

upper sequence: GRMZM2G149238_T04 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA09G41330.1 (Glycine max), 5'ss of exon 7

GACTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTAAAGTTTCCAATTAGGCTTGAGGGCCTTGCCTATTCTCATGGTGCCTTCTCAAGTgtatgtc-------caatgattgcttattttggcatcacaatttttttta----cctttttttttgtctcccttcttggaatttgacatttttcatttgttttacag
|| |||||||||||||| |||||||||||||||||||| ||||| || ||| | |||||||| ||||||||||| |||||||| |||||||||||| ||        |||| ||    | ||||  |     |||||  |  |       |  |       |||   | | | | |     |  | ||| || |      
GATTTTAAGATTCAGAACATTGTTGGCTCTTGTGATGTCAAGTTCCCCATTCGACTTGAGGGTCTTGCCTATTCCCATGGTGCTTTCTCAAGTgtaagtgtgaagtgcaataatcatctgtttttcctggtgaatttcatggaaaaatggtcctcacaaattcctgccctagtaatcag--tcctacatatggtc-----

upper sequence: GRMZM2G149238_T04 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA02G06370.1 (Glycine max), 5'ss of exon 3

GACTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTAAAGTTTCCAATTAGGCTTGAGGGCCTTGCCTATTCTCATGGTGCCTTCTCAAGTgtatgtccaatgattgcttattttggcatcacaattttttttacctttttt-tttgtctcccttcttggaatttgacatttttcatttgttttacag---
|| || || |||||||  ||||| |||||||||||||| ||||| || || | ||| ||||| ||||| ||||| |||||||| |||||||||||| ||       ||   | |||||| |  | ||||  |   |     ||  |   |      | ||  |     | ||||||  |||     |  |   
GATTTCAAAATTCAGATCATTGTCGGCTCTTGTGATGTCAAGTTCCCCAT-ATGCTGGAGGGTCTTGCATATTCCCATGGTGCTTTCTCAAGTgtaagtttttattttttattttttgggaaaataattcataggattggattggtccctggtgacttttatatcaaaatattttttgttttcacaatcgatg

upper sequence: GRMZM2G149238_T04 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA03G04500.1 (Glycine max), 5'ss of exon 7

GACTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTAAAGTTTCCAATTAGGCTTGAGGGCCTTGCCTATTCTCATGGTGCCTTCTCAAGTgtatgtccaatgattgcttattttggcatcacaattttttttacctttttttttgtctcccttcttggaatttgacatttttcatttgttttacag------------
|| || || |||||||| ||||| |||||||||||||| ||||| || ||  |||| ||||| ||||| ||||| |||||||| |||||||||||| ||    |  ||  ||  ||||| |  | ||||  |         ||  ||        | ||   |||  | ||||||  ||  ||| |||             
GATTTCAAAATTCAGAACATTGTCGGCTCTTGTGATGTCAAGTTCCCCATACGGCTGGAGGGTCTTGCATATTCCCATGGTGCTTTCTCAAGTgtaagt----tagttattt--tttgggaaaataattcatagggttggattggttactggtgatttttacatt--aaatttttttttgctttcacaatcaatgtttggc

upper sequence: GRMZM2G149238_T04 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA16G25450.3 (Glycine max), 5'ss of exon 7

GACTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTAAAGTTTCCAATTAGGCTTGAGGGCCTTGCCTATTCTCATGGTGCCTTCTCAAGTgtatgtccaatgattgcttattttggcatcacaattttttttacctttttttttg---tctcccttcttggaatttgacattt--ttcatttgttttacag-
|| || || |||||||| ||||| |||||||||||||| ||||| || ||  |||| ||||| ||||| ||||| |||||||| |||||||||||| ||    | |||  ||        |      |   |  |  ||||| | |     | |    | ||   | |  |  |||   |    || | |  || 
GATTTCAAAATTCAGAACATTGTCGGCTCTTGTGATGTCAAGTTCCCCATACGGCTGGAGGGTCTTGCATATTCCCATGGTGCTTTCTCAAGTgtaagttt--taattttttgggaaaataaattggtccctggtgacttttatatcagaatattttgttttcacaatcaatgtttggctatcctgatgtttagg

upper sequence: GRMZM2G149238_T04 (Zea mays), 5'ss of exon 6
lower sequence: AT3G13445.1 (Arabidopsis thaliana), 5'ss of exon 7

GACTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTAAAGTTTCCAATTAGGCTTGAGGGCCTTGCCTATTCTCATGGTGCCTTCTCAAGTgtatgtccaatga--ttgcttattttggcatcacaattt--tttttacctttttttttgtctcccttcttggaatttgacatttttcat-ttgttttacag----
|| || ||||||||||||||||| || ||||||||||| || || || || || ||||| || ||||| || ||||| | ||| |||||||||||  ||    | |  ||    |||| |   |||         |||||    |      ||    ||  | |  |||     | | |||| |||   |   |    
GATTTCAAGATTCAGAATATTGTAGGTTCTTGTGATGTCAAATTCCCTATAAGACTTGAAGGTCTTGCTTACTCTCACGCTGCTTTCTCAAGTgtgagtgatcttaacttatacatttagtagtcaaggaccgacttttagagataaaaacgttgtgctgatggccattacctctctctcatattggcgtgtggttag

upper sequence: GRMZM2G149238_T04 (Zea mays), 5'ss of exon 6
lower sequence: AT1G55520.1 (Arabidopsis thaliana), 5'ss of exon 7

GACTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTAAAGTTTCCAATTAGGCTTGAGGGCCTTGCCTATTCTCATGGTGCCTTCTCAAGTgtatgtccaatgattgcttattttggcatcaca-attttttttacctttttttttgtctcccttcttggaatttgacatttttcatttgttttacag-
|| |||||||| ||||| ||||| ||||| |||||||| || || || ||||||||||| || ||||| || |||||| |||| ||||||||||||     | ||||  |     |||  |||| | ||  || | || |   | ||  ||   ||  |  || |   || | | ||||   |  | |   
GATTTTAAGATACAGAACATTGTAGGCTCATGTGATGTCAAATTCCCCATTAGGCTTGAAGGTCTTGCATACTCTCATAGTGCTTTCTCAAGTgta-----agtgatctcaagcattgtgatcatatatacttgtaacatgggtgttaatcggtctgat--gattcatacctctctcatcattgatgccag

upper sequence: GRMZM2G149238_T04 (Zea mays), 5'ss of exon 6
lower sequence: Vv06s0004g00180.t01 (Vitis vinifera), 5'ss of exon 7

GACTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTAAAGTTTCCAATTAGGCTTGAGGGCCTTGCCTATTCTCATGGTGCCTTCTCAAGTgtatgtccaatgattgcttattttggcatcacaattttttttacctttttttttgtctcccttcttggaatttgacatttttcatttgttttacag--------
|| |||||||||||||| || |||||||| |||||||| || || || || |||||||| |||||||| ||||||||||||||||| || || ||| ||   ||||    || |||| | |   ||||| ||| |   ||||| | |       |       | |||  |  |    |||    ||  |        
GATTTTAAGATTCAGAACATAGTTGGCTCCTGTGATGTTAAATTCCCCATAAGGCTTGAAGGCCTTGCATATTCTCATGGTGCCTTTTCCAGCgtaagt--gatgaca--ttgttttcggagttcaattatttatttatttttctgtaaaaatgtgaaccatacttgggaagtcatgtttaaactaaggttggaaca

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|78084017|gb|DV512410.1|DV512410

EST:     TTCCAATTAGGCTTGAGGGCCTTGCCTATTCTCATGGTGCCTTCTCCAGT                         TACGAACCAGAACTCTTTCCTGGCCTTATCTATCGGATGAAACAACCAAAG
genomic: TTCCAATTAGGCTTGAGGGCCTTGCCTATTCTCATGGTGCCTTCTCAAGTgtatgtccaa ... tgttttacagTACGAACCAGAACTCTTTCCTGGCCTTATCTATCGGATGAAACAACCAAAG

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: 47 (upstream exon), 48 (downstream exon)
Score: 58

GACTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTAAAGTTTCCAATTAGGCTTGAGGGCCTTGCCTATTCTCATGGTGCCTTCTCAAGTgtatgtccaa ... tgttttacagTACGAACCAGAACTCTTTCCTGGCCTTATCTATCGGATGAAACAACCAAAGATTGTTCTTTTAATTTTTGTTTCAGGCAAGATTGTTTTGACTGGAGCAA

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 36

Block sizes: 47 (upstream exon), 45 (downstream exon)
Score: 25