ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

AGATATGGAGCTTGTGAGAGTGCTTCCTAGCGCTGAAGATGAAGTTAATGTTGCATGCTTTCATCCTTCACCAGGAGGTGGCCTTGTTTATGGCACTAAGgtcggtagaaaactattcaataaacaaagaggtatggcggattgctaaggctttcattctggtgaactatatag

Basic information

species	Zea mays
transcript	GRMZM2G007229_T01
intron #	13
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G007229_T01 (Zea mays), 5'ss of exon 13
lower sequence: LOC_Os02g18820.2 (Oryza sativa), 5'ss of exon 14

AGATATGGAGCTTGTGAGAGTGCTTCCTAGCGCTGAAGATGAAGTTAATGTTGCATGCTTTCATCCTTCACCAGGAGGTGGCCTTGTTTATGGCACTAAGgtcggtagaaaactat-tcaataaaca----aagaggtatggcggatt-gctaaggctttcattctggtgaactatatag-
 || |||||||| || ||||| |||||||| |||||||||||||| || |||||||||||||||||||| || |||||||| ||||||||||| || |||||   ||| ||| ||  ||||| ||||    |  |  |||    | || |||||  | | || ||     |  |  ||   
GGACATGGAGCTGGTAAGAGTTCTTCCTAGTGCTGAAGATGAAGTAAACGTTGCATGCTTTCATCCTTCCCCTGGAGGTGGTCTTGTTTATGGGACCAAGgtaaatagcaaattagatcaatcaacagtacacaacatatatttgctttgctaattcatgcactcacac-atttgcatcag

upper sequence: GRMZM2G007229_T01 (Zea mays), 5'ss of exon 13
lower sequence: GLYMA19G35370.1 (Glycine max), 5'ss of exon 12

AGATATGGAGCTTGTGAGAGTGCTTCCTAGCGCTGAAGATGAAGTTAATGTTGCATGCTTTCATCCTTCACCAGGAGGTGGCCTTGTTTATGGCACTAAGgtcggtagaaaactattcaataaacaaa-gaggtatggcggattgctaaggctttcattctggtgaactatatag---------------------------
||||||||| ||||| || ||||||||||| || |||||||| || ||||| ||||||||||||||||   | ||||| || || |||||||| || |||||    |      |  |    | || || | |||||||   |   ||   |||||   |    | || ||| ||                            
AGATATGGAACTTGTTAGGGTGCTTCCTAGTGCAGAAGATGAGGTCAATGTGGCATGCTTTCATCCTTTTGCCGGAGGAGGACTAGTTTATGGAACAAAGgt----atggtgttgctgggcagaccaatggggtatggtttagcactttagctttacattatttaaattatttaattgataatcttttgcatgtgattttag

upper sequence: GRMZM2G007229_T01 (Zea mays), 5'ss of exon 13
lower sequence: GLYMA03G32620.2 (Glycine max), 5'ss of exon 11

AGATATGGAGCTTGTGAGAGTGCTTCCTAGCGCTGAAGATGAAGTTAATGTTGCATGCTTTCATCCTTCACCAGGAGGTGGCCTTGTTTATGGCACTAAGgtcggtagaaaactattcaa--taaacaaagaggtatggcggattgctaaggctttcattctggtgaactatatag---------------------------
||||||||| ||||| || ||||||||||| || ||||| || || ||||| ||||||||||||||||   | || || || || |||||||| || |||||  || |         ||     | ||| | |||||||   |   ||   |||| || | |  | || ||| ||                            
AGATATGGAACTTGTTAGGGTGCTTCCTAGTGCAGAAGACGAGGTCAATGTGGCATGCTTTCATCCTTTTGCTGGGGGAGGACTAGTTTATGGAACAAAGgtatgttgttgctggggcagaccgaccaatggggtatggtttagcactttagcttacactatt-taaattatttaattgataatcttttgcatgtggttgtag

upper sequence: GRMZM2G007229_T01 (Zea mays), 5'ss of exon 13
lower sequence: AT5G43930.1 (Arabidopsis thaliana), 5'ss of exon 12

AGATATGGAGCTTGTGAGAGTGCTTCCTAGCGCTGAAGATGAAGTTAATGTTGCATGCTTTCATCCTTCACCAGGAGGTGGCCTTGTTTATGGCACTAAGgt---cggtagaaaactattcaataaacaaagaggtatgg-cggattgctaaggctttcatt-----ctggtgaactatatag-----------
||||||||||||||||||||| || || ||  | || |||||||| || ||||| || ||||||||||| || ||||| || ||||||||||| || |||||   |  ||   ||  |    || | | |  |   |||  ||| |||  ||     |||||     ||  |||   || |             
AGATATGGAGCTTGTGAGAGTACTGCCAAGTTCAGAGGATGAAGTGAACGTTGCGTGTTTTCATCCTTCTCCTGGAGGAGGTCTTGTTTATGGGACAAAGgtaaaccatattgaatcagatcattatcgattaacaatgttcggtttgggaatctgatcattatcgactcatgactcatgttttttttccgtag

upper sequence: GRMZM2G007229_T01 (Zea mays), 5'ss of exon 13
lower sequence: AT1G04140.2 (Arabidopsis thaliana), 5'ss of exon 12

AGATATGGAGCTTGTGAGAGTGCTTCCTAGCGCTGAAGATGAAGTTAATGTTGCATGCTTTCATCCTTCACCAGGAGGTGGCCTTGTTTATGGCACTAAGgtcggtagaaaactatt-caataaacaaagaggtatggcg---gattgctaag--gctttcattctggtgaactatatag-----
||||||||| || |||||||| ||||| ||| | || ||||||||||||||||| |||||||||||||| || || || || ||||| ||||| || |||||   ||       ||   |||    |||       ||||    | || | |   |  || ||  | |   | ||| ||      
AGATATGGAACTGGTGAGAGTACTTCCAAGCTCAGAGGATGAAGTTAATGTTGCTTGCTTTCATCCTTCTCCTGGGGGAGGTCTTGTCTATGGAACAAAGgtaattaatcctaaatcgtaatgtgaaaaacttctcggcgctaaaatgttgacttgtattgatatttgctcaatatttatctcag

upper sequence: GRMZM2G007229_T01 (Zea mays), 5'ss of exon 13
lower sequence: Vv07s0005g04630.t01 (Vitis vinifera), 5'ss of exon 12

AGATATGGAGCTTGTGAGAGTGCTTCCTAGCGCTGAAGATGAAGTTAATGTTGCATGCTTTCATCCTTCACCAGGAGGTGGCCTTGTTTATGGCACTAAGgtcggtagaaaactattcaataaacaaagaggtatggcggattgctaaggctttcattctggt-gaactatatag------------------------------------------------------
||||||||| ||||| ||||||||||| || ||||||||||| || ||||| || ||||||||||||| ||| ||||| || ||||| ||||| || |||||    |    | ||     |  | | |    |||      ||| |      |||| |    | |||  ||||                                                        
AGATATGGAACTTGTTAGAGTGCTTCCCAGTGCTGAAGATGAGGTCAATGTAGCTTGCTTTCATCCTTTACCTGGAGGAGGTCTTGTGTATGGAACCAAGgtgtacatctga-taccgtttggaaatatttttatttttatttgttctcttcttcaataaaatagaataatattaattttttcagcttatatccttacttctgtgtaattcttttgctgaaaattgcag

upper sequence: GRMZM2G007229_T01 (Zea mays), 5'ss of exon 13
lower sequence: Vv05s0077g00140.t01 (Vitis vinifera), 5'ss of exon 12

AGATATGGAGCTTGTGAGAGTGCTTCCTAGCGCTGAAGATGAAGTTAATGTTGCATGCTTTCATCCTTCACCAGGAGGTGGCCTTGTTTATGGCACTAAGgtcggtagaaaactattcaataaacaaagaggtatggcggattgctaaggctttcattctgg---tgaactatatag--------------
 |||||||| ||||||||||| |||||||| || || ||||| |||||||| || ||||||||||||||    |||||||||||||| ||||| || |||||    | || |  ||| |  |||   | |    |    | || ||   ||| |    |||    |  | |||  |               
TGATATGGAACTTGTGAGAGTTCTTCCTAGTGCAGAGGATGAGGTTAATGTAGCTTGCTTTCATCCTTCTGTTGGAGGTGGCCTTGTCTATGGAACGAAGgtgaaca-aataggattta--aaatggatattgcttcttggtttctgcagctgtttacctgaccttataatattcacttgctcaaatacag

upper sequence: GRMZM2G007229_T01 (Zea mays), 5'ss of exon 13
lower sequence: PP1S58_234V6.1 (Physcomitrella patens), 5'ss of exon 13

AGATATGGAGCTTGTGAGAGTGCTTCCTAGCGCTGAAGATGAAGTTAATGTTGCATGCTTTCATCCTTCACCAGGAGGTGGCCTTGTTTATGGCACTAAGgtcggtagaaaa-ctattcaataaacaa------agaggtatg-gcggattgctaaggctttcattctggtgaactatatag------------------
||||||||||||||||||||| ||||| || ||||| |||||||| ||||| || || ||||||||   |   || || || ||||| ||||| || |||||  || |     || |    |  || |      |||  |||| | | ||   |     ||  || ||| |  |  ||                      
AGATATGGAGCTTGTGAGAGTACTTCCCAGTGCTGAGGATGAAGTGAATGTGGCGTGTTTTCATCCCCAAGTTGGTGGCGGTCTTGTATATGGAACAAAGgtgagttgttcttctgtgttctggactagtatttagatatatgtgtgaatcagttgtagttctatactgtttgaagattcgttatctgagataaagtgtt

upper sequence: GRMZM2G007229_T01 (Zea mays), 5'ss of exon 13
lower sequence: PP1S150_95V6.1 (Physcomitrella patens), 5'ss of exon 12

AGATATGGAGCTTGTGAGAGTGCTTCCTAGCGCTGAAGATGAAGTTAATGTTGCATGCTTTCATCCTTCACCAGGAGGTGGCCTTGTTTATGGCACTAAGgtcggtagaaaactattcaataaacaaagaggta------tggcggattgctaaggctttcattctggtgaactatatag---------------------
|||||||||||||||||| ||  | ||||| ||||||||||| || ||||| || |||||||||||   |   || ||||| ||||  ||||| || |||||  || |  |    |    |   |||    |||      |  |  |||| || |  | || || || |     || ||                      
AGATATGGAGCTTGTGAGGGTATTACCTAGTGCTGAAGATGAGGTGAATGTGGCGTGCTTTCATCCCCAAGTTGGTGGTGGTCTTGCATATGGAACAAAGgtgagttgtgattcctctgtttttcaagccagtaataagttatcacattg-taggagtctccttttgttagtagatttattgtttaagctggaatattttg

upper sequence: GRMZM2G007229_T01 (Zea mays), 5'ss of exon 13
lower sequence: EFJ26270 (Selaginella moellendorffii), 5'ss of exon 13

AGATATGGAGCTTGTGAGAGTGCTTCCTAGCGCTGAAGATGAAGTTAATGTTGCATGCTTTCATCCTTCACCAGGAGGTGGCCTTGTTTATGGCACTAAGgt-cggtagaaaactattcaataaacaaagaggtatggcggattgctaaggctttcattctggtgaactatatag
|||| || | || ||| |||| || || || |||||||||||||||||||| || ||||||||||||  |   || || || |||||||| ||||| ||||| ||| |     |  |   ||  |  |   ||  |   | |    |||                          
AGATTTGAAACTAGTGCGAGTTCTCCCAAGTGCTGAAGATGAAGTTAATGTAGCGTGCTTTCATCCTCGAGTTGGCGGAGGGCTTGTTTACGGCACAAAGgttcggcaactttccttgagatggatgactcggcctaatgcacaaataacag-----------------------

upper sequence: GRMZM2G007229_T01 (Zea mays), 5'ss of exon 13
lower sequence: EFJ14567 (Selaginella moellendorffii), 5'ss of exon 12

AGATATGGAGCTTGTGAGAGTGCTTCCTAGCGCTGAAGATGAAGTTAATGTTGCATGCTTTCATCCTTCACCAGGAGGTGGCCTTGTTTATGGCACTAAGgtcggtagaaaactattcaataaacaaagaggtatggcggattgctaaggctttcattctggtgaactatatag
|||| || | || ||| |||| || || || |||||||||||||||||||| || ||||||||||||  |   || || || |||||||| ||||| |||||   | || |||| | |  || |   |  |    |||  | |||  |                          
AGATTTGAAACTAGTGCGAGTTCTCCCAAGTGCTGAAGATGAAGTTAATGTAGCGTGCTTTCATCCTCGAGTTGGCGGAGGGCTTGTTTACGGCACAAAGgt---ttgacaactttcctttagatggat-gactcggcctaatgcacaaataacag------------------

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|6020744|gb|AW065552.1|AW065552

EST:     TTGCATGCTTTCATCCTTCACCAGGAGGTGGCCTTGTTTATGGCACTAAG                         GAAGGGAAGCTCAGGATCCTTCAGCACAATGGCGCAGACATGACAAACATG
genomic: TTGCATGCTTTCATCCTTCACCAGGAGGTGGCCTTGTTTATGGCACTAAGgtcggtagaa ... aactatatagGAAGGGAAGCTCAGGATCCTTCAGCACAATGGCGCAGACATGACAAACATG

EST: gi|22935603|gb|BU571878.1|BU571878

EST:     TTGCATGCTTTCATCCTTCACCAGGAGGTGGCCTTGTTTATGGCACTAAG                         GAAGGGAAGCTCAGGATCCTTCAGCACAATG
genomic: TTGCATGCTTTCATCCTTCACCAGGAGGTGGCCTTGTTTATGGCACTAAGgtcggtagaa ... aactatatagGAAGGGAAGCTCAGGATCCTTCAGCACAATG

EST: gi|87155951|gb|DY400740.1|DY400740

EST:     TTGCATGCTTTCATCCTTCACCAGGAGGTGGCCTTGTTTATGGCACTAAG                         GAAGGGAAGCTCAGGATCCTTCAGCACAATGGCGCAGACATGACAAACATG
genomic: TTGCATGCTTTCATCCTTCACCAGGAGGTGGCCTTGTTTATGGCACTAAGgtcggtagaa ... aactatatagGAAGGGAAGCTCAGGATCCTTCAGCACAATGGCGCAGACATGACAAACATG

EST: gi|26560158|gb|CA832393.1|CA832393

EST:     TTGCATGCTTTCATCCTTCACCAGGAGGTGGCCTTGTTTATGGCACTAAG                         GAAGGGAAGCTCAGGATCCTTCAGCACAATGGCGCAGACATGACAAACAT
genomic: TTGCATGCTTTCATCCTTCACCAGGAGGTGGCCTTGTTTATGGCACTAAGgtcggtagaa ... aactatatagGAAGGGAAGCTCAGGATCCTTCAGCACAATGGCGCAGACATGACAAACAT

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), 45 (downstream exon)
Score: 63

AGATATGGAGCTTGTGAGAGTGCTTCCTAGCGCTGAAGATGAAGTTAATGTTGCATGCTTTCATCCTTCACCAGGAGGTGGCCTTGTTTATGGCACTAAGgtcggtagaa ... aactatatagGAAGGGAAGCTCAGGATCCTTCAGCACAATGGCGCAGACATGACAAACATGGGGGTGGGTTGCTTCATTGAGGAAAATATGGTTGAG

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 94

Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 78