ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

ATGGCCTCTTGTCAAGACCGGATCAGAGAATTCTTGTTCTTGCTGCAACCAACCGGCCTTTCGATCTTGATGAGGCTATAATCCGTAGGTTCGAGCGAAGgtttgtatatttcacccaaaatgctagtaacatttatgcatccctcaatttgttccctgagctgtgttctctttaattaacag

Basic information

species	Zea mays
transcript	GRMZM2G058491_T01
intron #	11
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G058491_T01 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os01g12660.1 (Oryza sativa), 5'ss of exon 11

ATGGCCTCTTGTCAAGACCGGATCAGAGAATTCTTGTTCTTGCTGCAACCAACCGGCCTTTCGATCTTGATGAGGCTATAATCCGTAGGTTCGAGCGAAGgtttgtatatttcaccca--aaatgctagtaacatttatgcatccctcaatttgttccctgagctgt--gttctctttaattaacag----------------------------
||||||||||||||||||| ||||| | ||||||||| |||||||| |||||||| || || ||||||||||| ||||| || || ||||| ||||| ||||||| || | |  |     | ||||||||  |  | ||   |  || || || ||    |  |  |  | |   |  || |  ||                             
ATGGCCTCTTGTCAAGACCAGATCAAAAAATTCTTGTCCTTGCTGCGACCAACCGACCCTTTGATCTTGATGAAGCTATCATTCGAAGGTTTGAGCGCAGgtttgcatctcttccttgctagatgctagtt-ctctcatctgtatctaaacttttttttagcccctttcgattgttccaagttccatgcctgagtgtattgccttgcttctttag

upper sequence: GRMZM2G058491_T01 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA10G37380.1 (Glycine max), 5'ss of exon 10

ATGGCCTCTTGTCAAGACCGGATCAGAGAATTCTTGTTCTTGCTGCAACCAACCGGCCTTTCGATCTTGATGAGGCTATAATCCGTAGGTTCGAGCGAAGgt----ttgtatatttcacccaaaat-gctagtaacatttatgcatccctcaatttgttccctgagctgtgttctctttaatt-aacag-----------
||||  | ||| ||| ||| | | || ||||||| |||||||||||||||||| |||| || || |||||||| || || ||  |  |||| ||||| ||||        |  |||  |  |   | |  |  | | | | |  ||  ||    |   | |   |||| | || |||||| |  ||||            
ATGGAATATTGACAAAACCTGGTGAGCGAATTCTGGTTCTTGCTGCAACCAACAGGCCATTTGACCTTGATGAAGCAATTATAAGACGGTTTGAGCGCAGgtaagaccacacctttgtcttatggttggcatgatcttctgttgattacttgtgtctgttcagcagctatattttctttattagaacaatcacaatcatt

upper sequence: GRMZM2G058491_T01 (Zea mays), 5'ss of exon 11
lower sequence: Vv16s0050g01850.t01 (Vitis vinifera), 5'ss of exon 13

ATGGCCTCTTGTCAAGACCGGATCAGAGAATTCTTGTTCTTGCTGCAACCAACCGGCCTTTCGATCTTGATGAGGCTATAATCCGTAGGTTCGAGCGAAGgt----ttgtatatttcacc--------caaaatgctagtaacatttatgcatccctcaatttgttccctgagctgtgttc---tctttaattaacag--
|||| ||  || ||| | | | | |  |||| ||||||||||||||||||||| |||| || || ||||| ||||| || ||| |  |||| ||||| ||||    |||||||||  |          ||  || ||  |    ||  ||||||||| ||| |    |   |     |  |   |||| |   ||     
ATGGGCTACTGACAAAAGCTGGTGAACGAATCCTTGTTCTTGCTGCAACCAACAGGCCATTTGACCTTGACGAGGCAATTATCAGGCGGTTTGAGCGCAGgtagatttgtatattgtattacactcagcatcattctcatcgttttactgcatcccttaatcttcaactacaaaaaaggccagatcttcatcaaagcatg

upper sequence: GRMZM2G058491_T01 (Zea mays), 5'ss of exon 11
lower sequence: Vv02s0025g00650.t01 (Vitis vinifera), 5'ss of exon 12

ATGGCCTCTTGTCAAGACCGGATCAGAGAATTCTTGTTCTTGCTGCAACCAACCGGCCTTTCGATCTTGATGAGGCTATAATCCGTAGGTTCGAGCGAAGgt--ttgtatatttcacccaaaatgctagtaacatttatgcatccctcaatttgttccctgagctgtgttctctttaattaacag-------------------
|||| |||||| ||| ||||| | || | |||||||||||||||||||| ||| |||| || || |||||||| || |||||| |  | || ||| | ||||   | |  |||||    || || | |   || || ||| |    | | ||           |  |||| ||||   | |  ||                   
ATGGACTCTTGACAAAACCGGGTGAGCGGATTCTTGTTCTTGCTGCAACTAACAGGCCATTTGACCTTGATGAAGCCATAATCAGACGCTTTGAGAGGAGgtaactctgcatttccaagaacattccacacaccttaatggaagtttgagttcaccttt----ccatgttttcttggttgaggaggagaagccaaaattattat

upper sequence: GRMZM2G058491_T01 (Zea mays), 5'ss of exon 11
lower sequence: Vv16s0050g01830.t01 (Vitis vinifera), 5'ss of exon 11

ATGGCCTCTTGTCAAGACCGGATCAGAGAATTCTTGTTCTTGCTGCAACCAACCGGCCTTTCGATCTTGATGAGGCTATAATCCGTAGGTTCGAGCGAAGgt----ttgtatatttcacccaaaatgctagtaacatttatgcatccctcaatttgttccctgagctgtgttctcttta-attaacag------------------------------------------------------------------
|||| ||  || ||| | | | | |  || | || |||||||||||||||||| |||| || || ||||||||||| || ||| |  |||| ||||  ||||    ||| |||||    |  |   |  | | |  || ||   |    |   ||    |   ||| ||||| | |  | |   | |                                                                   
ATGGACTACTGACAAAAGCTGGTGAACGAGTCCTCGTTCTTGCTGCAACCAACAGGCCATTTGACCTTGATGAGGCGATTATCAGGCGGTTTGAGCACAGgtagatttgcatattgtgtcacactcggca-tcattttcatcgttttaccgcatttaaactaaagccgtgttgtatggagaaggatatattgaagatagatgaatgtgtcaccatgcttcgagtaggcaaactaatggtatctgtgatgaacag

upper sequence: GRMZM2G058491_T01 (Zea mays), 5'ss of exon 11
lower sequence: Vv16s0050g01840.t01 (Vitis vinifera), 5'ss of exon 12

ATGGCCTCTTGTCAAGACCGGATCAGAGAATTCTTGTTCTTGCTGCAACCAACCGGCCTTTCGATCTTGATGAGGCTATAATCCGTAGGTTCGAGCGAAGgt----ttgtatatt---tcacccaaaatgctagtaacatttatgcatccctcaatttgttccctgagctgtgttctctttaattaacag------------------------------------------------
|||| ||  || ||| | | | | |  || | || |||||||||||||||||| |||| || || ||||||||||| || ||| |  |||| || |  ||||    ||| |||||   | || |  |     | |  |||   |  | | || ||  | |       | | | ||     ||  | |  |                                                
ATGGACTACTGACAAAAGCTGGTGAACGAGTCCTCGTTCTTGCTGCAACCAACAGGCCATTTGACCTTGATGAGGCGATTATCAGGCGGTTTGACCACAGgtagatttgcatattgtgttacactcagcatcattttcatcgtttta-ctctgaagctatggagaaggatatattaaagatagatgaatgtgtcaccatgctttgagtaggcaaactaatggtatctgtgatgaacag

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|61119440|gb|DN560401.1|DN560401

EST:     AACCGGCCTTTCGATCTTGATGAGGCTATAATCCGTAGGTTCGAGCGAAG                         AATCATGGTAGGTCTGCCATCGATGGGAAGTCGGGAACTCATAATGCGGCG
genomic: AACCGGCCTTTCGATCTTGATGAGGCTATAATCCGTAGGTTCGAGCGAAGgtttgtatat ... taattaacagAATCATGGTAGGTCTGCCATCGATGGGAAGTCGGGAACTCATAATGCGGCG

EST: gi|40335664|gb|CK369734.1|CK369734

EST:     AACCGGCCTTTCGATCTTGATGAGGCTATAATCCGTAGGTTCGAGCGAAG                         AATCATGGTAGGTCTGCCATCGATGGGAAGTCGGGAACTCATAATGCGGCG
genomic: AACCGGCCTTTCGATCTTGATGAGGCTATAATCCGTAGGTTCGAGCGAAGgtttgtatat ... taattaacagAATCATGGTAGGTCTGCCATCGATGGGAAGTCGGGAACTCATAATGCGGCG

EST: gi|94477011|gb|EB705969.1|EB705969

EST:     AATCCGTAGGTTCGAGCGAAG                         AATCATGGTAGGTCTGCCATCGATGGGAAGTCGGGAACTCATAATGCGGCG
genomic: AATCCGTAGGTTCGAGCGAAGgtttgtatat ... taattaacagAATCATGGTAGGTCTGCCATCGATGGGAAGTCGGGAACTCATAATGCGGCG

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 3 RNA-Seq libraries.

Block sizes: 49 (upstream exon), 39 (downstream exon)
Score: 35

ATGGCCTCTTGTCAAGACCGGATCAGAGAATTCTTGTTCTTGCTGCAACCAACCGGCCTTTCGATCTTGATGAGGCTATAATCCGTAGGTTCGAGCGAAGgtttgtatat ... taattaacagAATCATGGTAGGTCTGCCATCGATGGGAAGTCGGGAACTCATAATGCGGCGACTTCTGTCAAAGGAGAAAGTTGATGAAGGGCTGGACTTCAAGGAGCTA

Block sizes: 47 (upstream exon), 39 (downstream exon)
Score: 4