ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

CTAATTCAAAGCCTTGTCCCAAATGCAAGCGGCCTATTGAAAAAAATCAGGGATGCATGCACATCACATGCACTCCACCATGCAAATTTGAGTTCTGCTGgtaggcattctttcttttatacattttattcttattagttttagcaaatggaaaacatgatagttgtactatcatactacag

Basic information

species	Zea mays
transcript	GRMZM2G006428_T02
intron #	8
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G006428_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os04g41470.1 (Oryza sativa), 5'ss of exon 8

CTAATTCAAAGCCTTGTCCCAAATGCAAGCGGCCTATTGAAAAAAATCAGGGATGCATGCACATCACATGCACTCCACCATGCAAATTTGAGTTCTGCTGgtaggcattc---tttcttttatacattttattcttattagttttag---caaatggaaaacatgatagttgtactatcatactacag
||||||||||||||||||| || ||||||||||| ||||||||||| ||||||||||||||||| |||||||| || ||||||||||||||||| |||||||| | | ||    |   | | |  ||  | ||| ||  | ||  ||   || ||||     ||| || |||| |||| |||   |||
CTAATTCAAAGCCTTGTCCTAAGTGCAAGCGGCCCATTGAAAAAAACCAGGGATGCATGCACATTACATGCACACCTCCATGCAAATTTGAGTTTTGCTGgtatgtaatcataatctctctgtttatgctcttcatagcacttgcagtctcatatggcttgtatg-tacttgttctat-ataacgcag

upper sequence: GRMZM2G006428_T01 (Zea mays), 5'ss of exon 8
lower sequence: AT1G65430.1 (Arabidopsis thaliana), 5'ss of exon 8

CTAATTCAAAGCCTTGTCCCAAATGCAAGCGGCCTATTGAAAAAAATCAGGGATGCATGCACATCACATGCACTCCACCATGCAAATTTGAGTTCTGCTGgtaggc--attctttcttttatacattttattcttattagttttagcaaatg-gaaaacatgatagttgtactatc-atactacag---------------
| ||||| ||||| ||||| |||||||| ||||| || || ||||| ||||| || ||||| || || ||||| |||||||| |||||||||||||||||||| |   ||    |  || ||  |    | |  ||| | | | || |  |  |     ||  |   | ||||  |  || |  |                
CAAATTCCAAGCCCTGTCCAAAATGCAAACGGCCAATAGAGAAAAACCAGGGTTGTATGCATATTACGTGCACCCCACCATGTAAATTTGAGTTCTGCTGgtaagttgataaagtggttgattaaacaaaatgctat-aatgtcagaagttatgcttttattctctctatacttcctgtaatctaactctgaattggattc

upper sequence: GRMZM2G006428_T01 (Zea mays), 5'ss of exon 8
lower sequence: Vv00s0207g00090.t01 (Vitis vinifera), 5'ss of exon 8

CTAATTCAAAGCCTTGTCCCAAATGCAAGCGGCCTATTGAAAAAAATCAGGGATGCATGCACATCACATGCACTCCACCATGCAAATTTGAGTTCTGCTGgtaggcattctttcttttatacattttattcttattagt-tttagcaaatggaaaacatgatagttgtactatc-atactacag----------------
||||||| ||||||||||| || || |||||||| || |||||||| || || || ||||| ||||||||||| || ||||| ||||||||||| |||||||| |  |   | || || | |    ||  || |   || ||||| |  |        |  |   | |  |||| |     ||                 
CTAATTCCAAGCCTTGTCCAAAGTGTAAGCGGCCAATCGAAAAAAACCAAGGTTGTATGCATATCACATGCACACCGCCATGTAAATTTGAGTTTTGCTGgtaagtttatatactcttgttctagatagactcacatgtatttaggaggtctggtctttattccattttgtatccacttggcaacactagcattatcaag

upper sequence: GRMZM2G006428_T01 (Zea mays), 5'ss of exon 8
lower sequence: PP1S9_199V6.1 (Physcomitrella patens), 5'ss of exon 9

CTAATTCAAAGCCTTGTCCCAAATGCAAGCGGCCTATTGAAAAAAATCAGGGATGCATGCACATCACATGCACTCCACCATGCAAATTTGAGTTCTGCTGgtaggcattctttcttttatacattttattcttattagttttagcaaatggaaaacatgatagttgtactatcatactacag------------------------------------------------------------------------------------------------------------------------
| ||    || || ||||||||||| ||  |||| || ||||| ||||| || ||||||||||| || ||||| ||||| |||||||||||||| |||||||| | | |   |  |||   || || | ||| |  |||  | |   |||||  |      | |  |||  | ||  || ||                                                                                                                        
CGAACAGCAAACCCTGTCCCAAATGTAAAAGGCCAATCGAAAAGAATCAAGGCTGCATGCACATTACTTGCACACCACCTTGCAAATTTGAGTTTTGCTGgtaagtaatggataattt---caattgaatctaa--agtcatgg---atggatcatgattcattcttaccttaattttatagacacagctacttaagtttacgttgcttcactctgagtatgttgacaccagtggttggtaagtctatcacttataagcaaccaaatttattcactcagttttatttatgcgtttttgacag

upper sequence: GRMZM2G006428_T01 (Zea mays), 5'ss of exon 8
lower sequence: PP1S178_72V6.3 (Physcomitrella patens), 5'ss of exon 8

CTAATTCAAAGCCTTGTCCCAAATGCAAGCGGCCTATTGAAAAAAATCAGGGATGCATGCACATCACATGCACTCCACCATGCAAATTTGAGTTCTGCTGgtaggc----------attctttcttttata----------cattttatt---cttattagttttagcaaatggaaaacatgatagttgtactatcat-actacag--------------------------------------------------------------
| ||    || || || || ||||| ||| | || ||||||||||| || || |||||||| || || ||||| ||||| |||||||||||||| |||||||| |           |||||| ||||  |            | || |||    ||| || | |||  |  || ||  ||  ||  || ||   |||| |   |||                                                              
CAAACAGCAAACCCTGCCCTAAATGTAAGAGACCGATTGAAAAAAACCAAGGCTGCATGCATATTACTTGCACACCACCTTGCAAATTTGAGTTTTGCTGgtaagttgtaaatattattcttactttagttaaattaaagttacttaattggatttagtactattaatatgtgaaagtcaccatgcttataaggtcatcaactcagctgctgcaattcatgttgcctcattctcaagtgtagcttttgaaccttgacttctttggcag

upper sequence: GRMZM2G006428_T01 (Zea mays), 5'ss of exon 8
lower sequence: PP1S114_2V6.1 (Physcomitrella patens), 5'ss of exon 8

CTAATTCAAAGCCTTGTCCCAAATGCAAGCGGCCTATTGAAAAAAATCAGGGATGCATGCACATCACATGCACTCCACCATGCAAATTTGAGTTCTGCTGgtaggcattct----ttcttttataca-------ttttattcttattagttttagcaaa--tggaaaac--atgatagttgtactatcatactacag------------------------------------------------------------------------------------------------------
| ||    || ||||| ||||| || ||| |||| ||||| ||||| || || |||||||| ||||| ||||||||||| ||||||  |||||| ||||||||  || | |    |  ||||| | |       ||||||| |   |  ||  ||  ||  | |  |||  |||| | | |  ||  |  | ||                                                                                                         
CAAACAGCAAACCTTGCCCCAAGTGTAAGAGGCCAATTGAGAAAAACCAAGGCTGCATGCATATCACTTGCACTCCACCTTGCAAACATGAGTTTTGCTGgtaaacaatttaatgtaattttaaaaaaatagttttttattttcccttattgaagttaagcttgttaacgaatgaaattcggtcttgctcattaagctcatcagtgcagctgcggcagtccatgctattgtattttaacgctttgagtgtctggtttggaaatagtgtcacttacaagagttcactgatactataacag

upper sequence: GRMZM2G006428_T01 (Zea mays), 5'ss of exon 8
lower sequence: PP1S156_28V6.1 (Physcomitrella patens), 5'ss of exon 8

CTAATTCAAAGCCTTGTCCCAAATGCAAGCGGCCTATTGAAAAAAATCAGGGATGCATGCACATCACATGCACTCCACCATGCAAATTTGAGTTCTGCTGgtaggcattctttcttttatacattttattcttattagttttagcaaatggaaaacatgatagttgtactatcatactacag------------------------------------------------------------------------------------
| ||    || || || |||||||| ||  |||| ||||| ||||| || || || |||||||| || ||||| || || |||||||||||||| |||||||| |  |  |   ||||||    | |      || | |      ||||  |       |    |  |  ||  | ||  ||                                                                                    
CAAACAGCAAACCCTGCCCCAAATGTAAAAGGCCAATTGAGAAAAACCAAGGGTGTATGCACATTACTTGCACACCTCCTTGCAAATTTGAGTTTTGCTGgtaagtctaatagattttattgggtctcgaggaatgaatgggtttaaattcactctccaactcatcgataatggttcttaagtttttgttgctttagcctgaatgggttgaaagctggtcattgataagacacttacttatgagcaacccacttttgtttctaaag

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|76281609|gb|DV021177.1|DV021177

EST:     GGATGCATGCACATCACATGCACTCCACCATGCAAATTTGAGTTCTGCTG                         GCTATGTCTTGGTCCATGGTCAGAGCATGGAGAGAGGACTGGTGGATTTTA
genomic: GGATGCATGCACATCACATGCACTCCACCATGCAAATTTGAGTTCTGCTGgtaggcattc ... catactacagGCTATGTCTTGGTCCATGGTCAGAGCATGGAGAGAGGACTGGTGGATTTTA

EST: gi|211292139|gb|FL375498.1|FL375498

EST:     GGATGCATGCACATCACATGCACTCCACCATGCAAATTTGAGTTCTGCTG                         GCTATGTCTTGGTCCATGGTCAGAGCATGGAGAGAGGACTGGTGGATTTTA
genomic: GGATGCATGCACATCACATGCACTCCACCATGCAAATTTGAGTTCTGCTGgtaggcattc ... catactacagGCTATGTCTTGGTCCATGGTCAGAGCATGGAGAGAGGACTGGTGGATTTTA

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: 192

CTAATTCAAAGCCTTGTCCCAAATGCAAGCGGCCTATTGAAAAAAATCAGGGATGCATGCACATCACATGCACTCCACCATGCAAATTTGAGTTCTGCTGgtaggcattc ... catactacagGCTATGTCTTGGTCCATGGTCAGAGCATGGAGAGAGGACTGGTGGATTTTATGCTTGTAACCGCTATGAGTCAGCAAGGCAAGAAGGAGTG

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 188

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 151