ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

AGAATATGCTGTTGCAATCAAGAATGTGACAATAAATGATAACTTCTTCCCAGGGCATTTCCCTGAACGACCCATAATGCCTGGTGTTCTCATGGTCGAGgtatataatattctcgttatttttcctttttttgatacctacattgcttattgagatgcaattgtttcatcattattgacatgtagactaaagtgatgtt...

Basic information

species	Zea mays
transcript	GRMZM2G055667_T01
intron #	3
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G055667_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os05g36000.1 (Oryza sativa), 5'ss of exon 3

AGAATATGCTGTTGCAATCAAGAATGTGACAATAAATGATAACTTCTTCCCAGGGCATTTCCCTGAACGACCCATAATGCCTGGTGTTCTCATGGTCGAGgtatataatattctcgttatttttcctttttttgatacctacattgctta-ttgagatgcaattgtttcatcattattgacatgtagactaaagtgatgtt-
 |||||||||||||  ||||||||||| |||||||||||||||||||||||||||||||| || ||  |||| ||||||||||||||||| ||||| |||||||| | |  | | |||          ||| || | | ||  ||||||| || | ||  ||   ||||    || | |  |  |  |||   |      | 
GGAATATGCTGTTGGGATCAAGAATGTTACAATAAATGATAACTTCTTCCCAGGGCATTTTCCGGAGAGACCTATAATGCCTGGTGTTCTTATGGTGGAGgtatacattgattttgtttgccagtacgtttgtgtt-catatgttgcttaatttacatttaacaatttctaagttgtggttacttt-actggtgcttccctt

upper sequence: GRMZM2G055667_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA08G07870.1 (Glycine max), 5'ss of exon 3

AGAATATGCTGTTGCAATCAAGAATGTGACAATAAATGATAACTTCTTCCCAGGGCATTTCCCTGAACGACCCATAATGCCTGGTGTTCTCATGGTCGAGgtatataatattctcgttatttttcctttttttgatacctacattgcttattgagatgcaattgtttcatcattattgacatgtagactaaagtgatgtt-
||  | ||| || || || |||||||||||||||||||| ||||| || || |||||||| |||||| |||| || ||||||||||||||| |||| |||||| | | ||| ||     ||||   ||   ||      |   |||  |  |    || || | ||| ||  | |  |   |     ||    |    || 
AGTTTCTGCAGTGGCCATAAAGAATGTGACAATAAATGACAACTTTTTTCCTGGGCATTTTCCTGAAAGACCAATCATGCCTGGTGTTCTCCTGGTTGAGgtaaacactatgctgacccttttatattccctttccttttctcttgtcttcttgcctgaaactatttgattgtgaaag-tgtaagttctgtgctttaatta

upper sequence: GRMZM2G055667_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA15G05800.1 (Glycine max), 5'ss of exon 3

AGAATATGCTGTTGCAATCAAGAATGTGACAATAAATGATAACTTCTTCCCAGGGCATTTCCCTGAACGACCCATAATGCCTGGTGTTCTCATGGTCGAGgtatataatattctcgttatttttcctttttttgatacctacattgcttattgagatgcaattgtttcatcattat-tgacatgtagactaaagtgatgtt----
||  | ||| || || || |||||||||||||||||||| |||||||| || || ||||| || ||| | || || |||||||||||||| ||||||||||||  |||  |   |  | |  | | |  |       ||||| ||  ||||  |  |  |||| |||  || || | |    | || ||  | || ||| |    
AGTTTCTGCAGTGGCCATAAAGAATGTGACAATAAATGACAACTTCTTTCCTGGACATTTTCCAGAAAGGCCAATCATGCCTGGTGTTCTAATGGTCGAGgtac-taaactatacactgtgctgcttgctgcctgcccctacctttattat--atctctaattattttgtccttttcttgtctctaaac--atgttatggtaaaa

upper sequence: GRMZM2G055667_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA05G24650.1 (Glycine max), 5'ss of exon 3

------AGAATATGCTGTTGCAATCAAGAATGTGACAATAAATGATAACTTCTTCCCAGGGCATTTCCCTGAACGACCCATAATGCCTGGTGTTCTCATGGTCGAGgtatataatattctcgttattttt-cctttttttgatacctacattgcttattgaga--tgcaattgtttcatcat-tattgacatgtagactaaagtgatgtt
      ||  | ||| || || || |||||||||||||||||||| ||||| || || |||||||| || ||| |||| || ||||||||||||||||||||  ||||| | | || | |   | |   | || |||| |  | |||  ||    | || |    ||||||| ||| ||||  | |  | || |   ||           
TCCTGGAGTTTCTGCAGTGGCCATAAAGAATGTGACAATAAATGACAACTTTTTTCCTGGGCATTTTCCAGAAAGACCAATCATGCCTGGTGTTCTCATGgtttaggtaaacactaatatgagtctagctacccttttatatttcctttatattctcttcatgcctgcaatttttttatcaagtgtaaaaatctgtgctt----------

upper sequence: GRMZM2G055667_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA08G19200.1 (Glycine max), 5'ss of exon 2

AGAATATGCTGTTGCAATCAAGAATGTGACAATAAATGATAACTTCTTCCCAGGGCATTTCCCTGAACGACCCATAATGCCTGGTGTTCTCATGGTCGAGgtatataatattctcgttatttttcctttttttgatacctacattgcttattgagatgcaattgtttcatcattattgacatg-tagactaaagtgatgtt-
||  | ||| || || || |||||||||||||||||||| |||||||| || || ||||| || ||| | ||||| |||||||||||||| ||||| ||||||  ||| ||   |  |||  | |||   |||| |   |   ||  |||||  |         | ||   |    || |||| || | |  | | |  || 
AGTTTCTGCAGTGGCTATAAAGAATGTGACAATAAATGACAACTTCTTTCCTGGACATTTTCCAGAAAGGCCCATCATGCCTGGTGTTCTAATGGTTGAGgtac-taaaatatgcactatgct-cctacctttgttgtatctcttatttattttgtccttgccttgtctctaaacatgtcatgataaaatggaatcaatttg

upper sequence: GRMZM2G055667_T01 (Zea mays), 5'ss of exon 3
lower sequence: AT2G22230.1 (Arabidopsis thaliana), 5'ss of exon 3

AGAATATGCTGTTGCAATCAAGAATGTGACAATAAATGATAACTTCTTCCCAGGGCATTTCCCTGAACGACCCATAATGCCTGGTGTTCTCATGGTCGAGgtatataatattctcgttatttttcctttttttgatacctacattgcttattgagatgcaattgtttcatcattattgacatgtagactaaagtgatgtt-
 |  |  ||||| || || |||||||| || || ||||| || |||||||| || ||||||||||||||||| || |||||||||||||||||| | |||||| |||||| ||   | |  || |    |||||    | | |      | |    || ||||| |   | |    |   ||       ||| || | |  
TGTTTCAGCTGTAGCTATTAAGAATGTCACCATCAATGACAATTTCTTCCCTGGCCATTTCCCTGAACGACCAATCATGCCTGGTGTTCTCATGATTGAGgta-ataataatcgtttaaagttgcaaacttttgtcctcaagaagatcaaatattttgtaattgatatgttagctgttgtattcctttcaaaatgctttaa

upper sequence: GRMZM2G055667_T01 (Zea mays), 5'ss of exon 3
lower sequence: AT5G10160.1 (Arabidopsis thaliana), 5'ss of exon 3

AGAATATGCTGTTGCAATCAAGAATGTGACAATAAATGATAACTTCTTCCCAGGGCATTTCCCTGAACGACCCATAATGCCTGGTGTTCTCATGGTCGAGgtatataatattctcgttatttttcctttttttgatacctacattgcttattgagatgcaattgtttcatcattattgacatgtagactaaagtgatgtt
 | || ||| || || || || || || || || ||||| || ||||| || ||||||||||||||  |||| ||||||||||| ||||||||||| ||||||  |   |||  |  |||| |  ||| ||     |           | ||   ||  | || |      |  |    | | | ||    ||  || | 
TGTATCTGCGGTAGCTATTAAAAACGTTACCATTAATGACAATTTCTTTCCTGGGCATTTCCCTGAGAGACCTATAATGCCTGGAGTTCTCATGGTTGAGgtaatttgcatttgccctattctctcttcttactccaaaagttcaatctgtttgcatatatttatagttaaaagagaagctttttgagcctagacattta

upper sequence: GRMZM2G055667_T01 (Zea mays), 5'ss of exon 3
lower sequence: Vv12s0055g01100.t01 (Vitis vinifera), 5'ss of exon 3

AGAATATGCTGTTGCAATCAAGAATGTGACAATAAATGATAACTTCTTCCCAGGGCATTTCCCTGAACGACCCATAATGCCTGGTGTTCTCATGGTCGAGgta-tataatattctcgttattttt------cctttttttgatacctacattgcttattgagatgcaattgtttcatcattattgacatgtagactaaagtgatgtt
||  | ||||||||| || |||||||| |||||||||||||||||||| || |||||||| || ||  | || || |||||||||||||||||||| |||||| | |  | ||| |||   ||||        ||||||   ||  | ||||  || |  || | ||  | |    | | | ||  ||| |   ||| |        
AGTTTCTGCTGTTGCCATAAAGAATGTAACAATAAATGATAACTTCTTTCCTGGGCATTTTCCCGAGAGGCCAATTATGCCTGGTGTTCTCATGGTTGAGgtaatttcttgttcccgtaccttttaaatatttttttttctttagttgcattatttttaaagttacatgtatgaggtaaatgtttccatttttgctacaa-------

upper sequence: GRMZM2G055667_T01 (Zea mays), 5'ss of exon 3
lower sequence: Vv00s0357g00070.t01 (Vitis vinifera), 5'ss of exon 3

AGAATAT--GCTGTTGCAATCAAGAATGTGACAATAAATGATAACTTCTTCCCAGGGCATTTCCCTGAACGACCCATAATGCCTGGTGTTCTCATGGTCGAGgtatataatattctcgttatttttcctttttttgatacctacattgcttattgagatgcaattgtttcatcattattgacatgtagactaaagtgatgtt-
 | || |  ||  | ||||| ||||||||||| ||||   |||||||||| || ||||| ||||||||  | || || ||||||||||| |||||||| |||||| ||    || | |  |   ||  | || || ||    |      ||| |   |   ||  |        | |   | |   |     |  |  |  | 
-GGATCTCAGCAATAGCAATTAAGAATGTGACTATAA-CAATAACTTCTTTCCTGGGCACTTCCCTGAGAGGCCAATTATGCCTGGTGTGCTCATGGTTGAGgta-atttgcttattgccaaactttatgttcttcatttgaattcaatttactagaaaataaaagaaaatgtttgaaaaataaagaactcgacatatttgtg

upper sequence: GRMZM2G055667_T01 (Zea mays), 5'ss of exon 3
lower sequence: Vv00s0357g00020.t01 (Vitis vinifera), 5'ss of exon 3

AGAATATGCTGTTGCAATCAAGAATGTGACAATAAATGATAACTTCTTCCCAGGGCATTTCCCTGAACGACCCATAATGCCTGGTGTTCTCATGGTCGAGgtatataatattctcgttatttttcctttttttgatacctacattgcttattgagatgcaattgtttcatcattattgacatgtagactaaagtgatgtt-
    |  || || ||||| ||||||||||| ||||| ||||||||||| || ||||| ||||||||  | || || ||||||||||| |||||||| |||||| ||    || | |  |   ||| | || || ||    |      ||| |   |   ||  |        | |   | |   |    ||  |  |  | 
GATCTCAGCAGTAGCAATTAAGAATGTGACTATAAACGATAACTTCTTTCCTGGGCACTTCCCTGAGAGGCCAATTATGCCTGGTGTGCTCATGGTTGAGgta-atttgcttattgccaaacttcatgttcttcatttgaattcaatttactagaaaataacagaaaatgtttgaaaaataaagaactcaacatatttgtg

upper sequence: GRMZM2G055667_T01 (Zea mays), 5'ss of exon 3
lower sequence: PP1S196_99V6.1 (Physcomitrella patens), 5'ss of exon 1

AGAATATGCTGTTGCAATCAAGAATGTGACAATAAATGATAACTTCTTCCCAGGGCATTTCCCTGAACGACCCATAATGCCTGGTGTTCTCATGGTCGAGgtatataatattctcgttatttttcctttttttgatacctacattgcttattgagatgcaattgtttca--tcattattgacatgtagactaaagtgatgtt-
 || |  |||||||| || || |||||||| || ||||| ||||||||||| || || |||||  | || ||||| |||||||| || |||||||| ||||||     |  | ||     |||   |  | ||||||   |  |  |  ||||   |||   || || |  ||| || ||  ||   |     | |  | || 
GGAGTCGGCTGTTGCCATAAAAAATGTGACTATCAATGACAACTTCTTCCCTGGTCACTTCCCCCAGCGGCCCATCATGCCTGGGGTGCTCATGGTAGAGgtaagacgtcatttcagggatttga-tcatcttgatatgaatgtaac--attgcagtgcgcatggtttaggtcaataatgtaatagtgtgggcatttctattt

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|211366504|gb|FL067546.1|FL067546

EST:     AGGGCATTTCCCTGAACGACCCATAATGCCTGGTGTTCTCATGGTCGAAG                         GCAATGGCCCAGGTCGGAGGAATAGTGATGTTGCAGCCTGAAAGTGGGTG
genomic: AGGGCATTTCCCTGAACGACCCATAATGCCTGGTGTTCTCATGGTCGA-Ggtatataata ... gatttttcagGCAATGGCCCAGGTCGGAGGAATAGTGATGTTGCAGCCTGAA-GTGGGTG

EST: gi|149001245|gb|EE038521.2|EE038521

EST:     CAGGGCATTTTCCTGAACGACCCATACTGCCTGGTGTTCTCATGGTCGAG                         GCAATGGCCCAGGTCGGAGGAATAGTGATGTTG
genomic: CAGGGCATTTCCCTGAACGACCCATAATGCCTGGTGTTCTCATGGTCGAGgtatataata ... gatttttcagGCAATGGCCCAGGTCGGAGGAATAGTGATGTTG

EST: gi|149076117|gb|EE164700.2|EE164700

EST:     CAGGGCATTTCCCTGAACGACCCATAATGCCTGGTGTTCTCATGGTCGAG                         GCAATGGCCCAGGTCGGAGGAATAGTGATGTTGCAGCCTGAAGTGGGTGGA
genomic: CAGGGCATTTCCCTGAACGACCCATAATGCCTGGTGTTCTCATGGTCGAGgtatataata ... gatttttcagGCAATGGCCCAGGTCGGAGGAATAGTGATGTTGCAGCCTGAAGTGGGTGGA

EST: gi|211366505|gb|FL067547.1|FL067547

EST:     CAGGGCATTTCCCTGAACGACCCATAATGCCTGGTGTTCTCATGGTCGAG                         GGCA-TGGCCCAGGTCGGAAGAATAGTGAT
genomic: CAGGGCATTTCCCTGAACGACCCATAATGCCTGGTGTTCTCATGGTCGAGgtatataata ... gatttttcagG-CAATGGCCCAGGTCGGAGGAATAGTGAT

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: 45 (upstream exon), 47 (downstream exon)
Score: 21

AGAATATGCTGTTGCAATCAAGAATGTGACAATAAATGATAACTTCTTCCCAGGGCATTTCCCTGAACGACCCATAATGCCTGGTGTTCTCATGGTCGAGgtatataata ... gatttttcagGCAATGGCCCAGGTCGGAGGAATAGTGATGTTGCAGCCTGAAGTGGGTGGATCTCGAGAGAACTTCTTTTTTGCGGGGATCGATAAAGTGAGGTTCCGGA

Block sizes: 41 (upstream exon), 43 (downstream exon)
Score: 19

Block sizes: 40 (upstream exon), 48 (downstream exon)
Score: 12