ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GCACTTGACACGTTCAACACGGCAATTGTATCTCCAATATATTATGTAATGTTCACAACTCTTACAATACTTGCCAGCGTCATAATGTTCAAGgtaaattttgttttgcctttggcttatatatttattgcttatttcattctgcaatttactccctcatgcaccttttggaccctttcagatattttcatattgttgtatttgtttcatatgcattcctcagctctagtattatttgacaaaaccgtaaactgatgccatgctgtttaaatgtttgtgtag

Basic information

species	Zea mays
transcript	GRMZM2G120175_T04
intron #	7
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G120175_T04 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os05g43790.2 (Oryza sativa), 5'ss of exon 7

GCACTTGACACGTTCAACACGGCAATTGTATCTCCAATATATTATGTAATGTTCACAACTCTTACAATACTTGCCAGCGTCATAATGTTCAAGgtaaattttgttttgcctttggcttatatatttattgcttatttcattctgcaatttactccctcatgcaccttttggaccctttcagatattttcatattgttgtatttgtttcatatgcattcctcagctctagtattatttgacaaaaccgtaaactgatgccatgctgtttaaatgtttgtgtag
|||||||| || || || || ||||||||||||||||| |||||||||||||||||||| || ||||||||||| ||||||||||||||||||||||  |  ||| |    ||  ||| ||          | ||||  |     | || | | ||  |   |  || || |         ||||  |   |||                                                                                        
GCACTTGATACATTTAATACTGCAATTGTATCTCCAATCTATTATGTAATGTTCACAACACTAACAATACTTGCAAGCGTCATAATGTTCAAGgtaatataagttcttttgtttccttgtactgcagccattcatttggtagatgatttgaatgcccaagttattttctgaaagaaactgaatatccttg-att----------------------------------------------------------------------------------------

upper sequence: GRMZM2G120175_T04 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA02G44980.2 (Glycine max), 5'ss of exon 6

GCACTTGACACGTTCAACACGGCAATTGTATCTCCAATATATTATGTAATGTTCACAACTCTTACAATACTTGCCAGCGTCATAATGTTCAAGgtaaattttgttttgcctttggcttatatatttattgcttatttcattctgcaatttactccctcatgcaccttttggaccctttcagatattttcatattgttgtatttgtttcatatgcattcctcagctctagtattatttgacaaaaccgtaaactgatgccatgctgtttaaatgtttgtgtag
|| |||||||| |||||||| |||||||||||||| ||||| ||||| ||||||||||| ||||||||||| ||||| || |||||||| |||||| | |   ||     ||||||      ||||| |||| | | |||       ||   |     | | |   |       | |    | ||||  | ||  |  |    |                                                                              
GCTCTTGACACCTTCAACACAGCAATTGTATCTCCTATATACTATGTCATGTTCACAACACTTACAATACTAGCCAGTGTAATAATGTTTAAGgtataatcaatt--agttttggc------atttaatgctaaatgcataagatgtttctgttgtctacggattgtacaagaacctatttacatttaaaaataatgcttacag------------------------------------------------------------------------------

upper sequence: GRMZM2G120175_T04 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA14G03790.1 (Glycine max), 5'ss of exon 7

GCACTTGACACGTTCAACACGGCAATTGTATCTCCAATATATTATGTAATGTTCACAACTCTTACAATACTTGCCAGCGTCATAATGTTCAAGgtaaattttgttttgcctttggcttatatatttattgcttatttcattctgcaatttactccctcatgcaccttttggaccctttcagatattttcatattgttgtatttgtttcatatgcattcctcagctctagtattatttgacaaaaccgtaaactgatgccatgctgtttaaatgtttgtgtag
|| |||||||| |||||||| |||||||||||||| ||||| ||||| ||||||||||| ||||||||||| ||||| || |||||||| |||||| | |    |     ||||||      ||||| |||| | | |||       ||   |     | | |   |       | |    | ||||  | ||  |  |    |                                                                              
GCTCTTGACACCTTCAACACAGCAATTGTATCTCCTATATACTATGTCATGTTCACAACACTTACAATACTAGCCAGTGTAATAATGTTTAAGgtataatcaact--agttttggc------atttaatgctaaatgcataagatgtttctgttgtctacgaattgtacaagaacctatttacatttaaaaataatgcttacag------------------------------------------------------------------------------

upper sequence: GRMZM2G120175_T04 (Zea mays), 5'ss of exon 7
lower sequence: Vv06s0009g03650.t01 (Vitis vinifera), 5'ss of exon 7

GCACTTGACACGTTCAACACGGCAATTGTATCTCCAATATATTATGTAATGTTCACAACTCTTACAATACTTGCCAGCGTCATAATGTTCAAGgtaaattttgttttgcctttggc-ttatatatt---tattgcttatttcattctgcaatttactccctcatgcaccttttggaccctttcagatattttcatattgttgtatttgtttcatatgcattcctcagctctagtattatttgacaaaaccgtaaactgatgccatgctgtttaaatgtttgtgtag
|| ||||| || |||||||| ||| |||| || || ||||||||||| ||||||||| | |||||||| ||||| || || |||||||||||||||   | |  |||  |  |||| |  |||  |   |  || ||  | ||  ||  || ||  |  |  ||  | |||     |  ||| || | ||    ||||                                                                                        
GCTCTTGATACTTTCAACACTGCAGTTGTGTCCCCCATATATTATGTCATGTTCACATCACTTACAATCCTTGCTAGTGTGATAATGTTCAAGgtattgtcttctttatcagtggcatcttatgctggatgctgtttcctccaacctataactttttagcaaatatagctt-----catttttaggt-ttgctttatta---------------------------------------------------------------------------------------

upper sequence: GRMZM2G120175_T04 (Zea mays), 5'ss of exon 7
lower sequence: PP1S49_181V6.2 (Physcomitrella patens), 5'ss of exon 7

GCACTTGACACGTTCAACACGGCAATTGTATCTCCAATATATTATGTAATGTTCACAACTCTTACAATACTTGCCAGCGTCATAATGTTCAAGgtaaattttgttttgcctttggcttatatatttattgcttatttcattctgcaat--ttactccctcatgcaccttttggaccctttcagatattttcatattgttgtatttgtttcatatgcattcctcagctctagtattatttgacaaaaccgtaaactgatgccatgctgtttaaatgtttgtgtag
|| || ||||| || |||||||||||||| ||||| |||||||| || ||||||||| |  | || || || || || |  || |||||||||||   |  ||      ||     |  ||   || |      |||    |  ||||   |  |     | | |  | |  ||   |    |||   | ||                                                                                            
GCCCTGGACACATTTAACACGGCAATTGTTTCTCCTATATATTACGTCATGTTCACATCATTGACCATCCTGGCGAGTGCTATCATGTTCAAGgtttgtgctgacgctactagcaatcctaccattgtcaaa-gtttagagcaacaatatctgtttttctaagtaggtctgtgaagatgattgatccgtacacc------------------------------------------------------------------------------------------

upper sequence: GRMZM2G120175_T04 (Zea mays), 5'ss of exon 7
lower sequence: EFJ37634 (Selaginella moellendorffii), 5'ss of exon 7

GCACTTGACACGTTCAACACGGCAATTGTATCTCCAATATATTATGTAATGTTCACAACTCTTACAATACTTGCCAGCGTCATAATGTTCAAGgtaaattttgttttgcctttggcttatatatttattgcttatttcattctgcaatt-tactccctcatgcaccttttggaccctttcagatattttcatattgttgtatttgtttcatatgcattcctcagctctagtattatttgacaaaaccgtaaactgatgccatgctgtttaaatgtttgtgtag
||||| ||||| |||||||| || || || |||||| | || || || ||||||||| | || ||||| || || ||||| ||||||||||||||||     | |  |   |   | | |  |  |  ||  |  ||| |   |||||| ||    ||||  ||                                                                                                                       
GCACTCGACACTTTCAACACTGCCATCGTTTCTCCAGTCTACTACGTCATGTTCACAGCGCTGACAATCCTCGCGAGCGTGATAATGTTCAAGgtaa--cacgctcagttctctccct-tggacctgatgaatgattcgtg--gcaattatagctactcacacag----------------------------------------------------------------------------------------------------------------------

upper sequence: GRMZM2G120175_T04 (Zea mays), 5'ss of exon 7
lower sequence: EFJ15054 (Selaginella moellendorffii), 5'ss of exon 7

GCACTTGACACGTTCAACACGGCAATTGTATCTCCAATATATTATGTAATGTTCACAACTCTTACAATACTTGCCAGCGTCATAATGTTCAAGgtaaattttgttttgcctttggcttatatatttattgcttatttcattctgcaatttactccctcatgcaccttttggaccctttcagatattttcatattgttgtatttgtttcatatgcattcctcagctctagtattatttgacaaaaccgtaaactgatgccatgctgtttaaatgtttgtgtag
||||| ||||| |||||||| || || || |||||| | || || || ||||||||| | || ||||| || || ||||| ||||||||||||||||     | |  |   |   ||| |  |  |  ||  |  ||| |     | | ||    ||||  ||                                                                                                                       
GCACTCGACACTTTCAACACTGCCATCGTTTCTCCAGTCTACTACGTCATGTTCACAGCGCTGACAATCCTCGCGAGCGTGATAATGTTCAAGgtaa--cacgctcagttctctcctt-tggacctgatgaatgattcgtgtca-attatagctactcacacag----------------------------------------------------------------------------------------------------------------------

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|101381796|gb|EB812955.1|EB812955

EST:     ATGTAATGTTCACAACTCTTACAATACTTGCCAGCGTCATAATGTTCAAG                         GATTGGTCTGGTCAAAGCCCTGGAAGCGTCATTTCTGAAATTTGTGGCTTG
genomic: ATGTAATGTTCACAACTCTTACAATACTTGCCAGCGTCATAATGTTCAAGgtaaattttg ... gtttgtgtagGATTGGTCTGGTCAAAGCCCTGGAAGCGTCATTTCTGAAATTTGTGGCTTG

EST: gi|60354097|gb|DN221070.1|DN221070

EST:     ATGTAATGTTCACAACTCTTACAATACTTGCCAGCGTCATAATGTTCAAG                         GATTGGTCTGGTCAAAGCCCTGGAAGCGTCATTTCTGAAATTTGTGGCTTG
genomic: ATGTAATGTTCACAACTCTTACAATACTTGCCAGCGTCATAATGTTCAAGgtaaattttg ... gtttgtgtagGATTGGTCTGGTCAAAGCCCTGGAAGCGTCATTTCTGAAATTTGTGGCTTG

EST: gi|78120401|gb|DV538785.1|DV538785

EST:     ATGTAATGTTCACAACTCTTACAATACTTGCCAGCGTCATAATGTTCAAG                         GATTGGTCTGGTCAAAGCCCTGGAAGCGTCATTTCTGAAATTTGTGGCTTG
genomic: ATGTAATGTTCACAACTCTTACAATACTTGCCAGCGTCATAATGTTCAAGgtaaattttg ... gtttgtgtagGATTGGTCTGGTCAAAGCCCTGGAAGCGTCATTTCTGAAATTTGTGGCTTG

EST: gi|148934735|gb|EC878784.2|EC878784

EST:     ATGTAATGTTCACAACTCTTACAATACTTGCCAGCGTCATAATGTTCAAG                         GATTGGTCTGGTCAAAGCCCTGGAAGCGTCATTTCTGAAATTTGTGGCTTG
genomic: ATGTAATGTTCACAACTCTTACAATACTTGCCAGCGTCATAATGTTCAAGgtaaattttg ... gtttgtgtagGATTGGTCTGGTCAAAGCCCTGGAAGCGTCATTTCTGAAATTTGTGGCTTG

EST: gi|74234882|gb|DT642796.1|DT642796

EST:     ATGTAATGTTCACAACTCTTACAATACTTGCCAGCGTCATAATGTTCAAG                         GATTGGTCTGGTCAAAGCCCTGGAAGCGTCATTTCTGAAATTTGTGGCTTG
genomic: ATGTAATGTTCACAACTCTTACAATACTTGCCAGCGTCATAATGTTCAAGgtaaattttg ... gtttgtgtagGATTGGTCTGGTCAAAGCCCTGGAAGCGTCATTTCTGAAATTTGTGGCTTG

EST: gi|148943740|gb|EC888810.2|EC888810

EST:     ATGTAATGTTCACAACTCTTACAATACTTGCCAGCGTCATAATGTTCAAG                         GATTGGTCTGGTCAAAGCCCTGGAAGCGTCATTTCTGAAATTTGTGGCTTG
genomic: ATGTAATGTTCACAACTCTTACAATACTTGCCAGCGTCATAATGTTCAAGgtaaattttg ... gtttgtgtagGATTGGTCTGGTCAAAGCCCTGGAAGCGTCATTTCTGAAATTTGTGGCTTG

EST: gi|149085220|gb|EE174728.2|EE174728

EST:     ATGTAATGTTCACAACTCTTACAATACTTGCCAGCGTCATAATGTTCAAG                         GATTGGTCTGGTCAAAGCCCTGGAAGCGTCATTTCTGAAATTTGTGGCTTG
genomic: ATGTAATGTTCACAACTCTTACAATACTTGCCAGCGTCATAATGTTCAAGgtaaattttg ... gtttgtgtagGATTGGTCTGGTCAAAGCCCTGGAAGCGTCATTTCTGAAATTTGTGGCTTG

EST: gi|76287457|gb|DV027025.1|DV027025

EST:     ATGTAATGTTCACAACTCTTACAATACTTGCCAGCGTCATAATGTTCAAG                         GATTGGTCTGGTCAAAGCCCTGGAAGCGTCATTTCTGAAATTTGTGGCTTG
genomic: ATGTAATGTTCACAACTCTTACAATACTTGCCAGCGTCATAATGTTCAAGgtaaattttg ... gtttgtgtagGATTGGTCTGGTCAAAGCCCTGGAAGCGTCATTTCTGAAATTTGTGGCTTG

EST: gi|211152612|gb|FL453073.1|FL453073

EST:     TGCCAGCGTCATAATGTTCAAG                         GATTGGTCTGGTCAAAGCCCTGGAAGCGTCATTTCTGAAATTTGTGGCTTG
genomic: TGCCAGCGTCATAATGTTCAAGgtaaattttg ... gtttgtgtagGATTGGTCTGGTCAAAGCCCTGGAAGCGTCATTTCTGAAATTTGTGGCTTG

EST: gi|166680559|gb|EG262871.1|EG262871

EST:     ATGTAATGTTCACAACTCTTACAATACTTGCCAGCGTCATAATGTTCAAG                         GATTGGTCTGGTCAAAG
genomic: ATGTAATGTTCACAACTCTTACAATACTTGCCAGCGTCATAATGTTCAAGgtaaattttg ... gtttgtgtagGATTGGTCTGGTCAAAG

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: 48 (upstream exon), 49 (downstream exon)
Score: 73

GCACTTGACACGTTCAACACGGCAATTGTATCTCCAATATATTATGTAATGTTCACAACTCTTACAATACTTGCCAGCGTCATAATGTTCAAGgtaaattttg ... gtttgtgtagGATTGGTCTGGTCAAAGCCCTGGAAGCGTCATTTCTGAAATTTGTGGCTTGGTTGTGGTGTTGTCTGGTACCATTTTGTTGCATGTGACGAAGGATTATG

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 166

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 221