ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

ACTTACTGAAGCTGGTAGTGACCGTGTCATTGTATGTGATATTCATTCTACGCAAGCGTTGGGGTACTTCGATATTCCTGTGGATCATATATATGGACAGgtagtgtgagttcttcctttacagcgtttgatttcagtattgcatctcgttgtaaattctatctgactacgaattagtgtcatccttggtgtctgtag

Basic information

species	Zea mays
transcript	GRMZM2G180863_T01
intron #	4
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G180863_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os06g41360.1 (Oryza sativa), 5'ss of exon 4

ACTTACTGAAGCTGGTAGTGACCGTGTCATTGTATGTGATATTCATTCTACGCAAGCGTTGGGGTACTTCGATATTCCTGTGGATCATATATATGGACAGgtagtgtgag------------ttcttcctttacagcgt-----ttgatttcagtattgc---atctcgttg--taaattctatctgactacgaattagtgtc---atccttggtgtctgtag
|||||| |||||||| ||||| ||||| |||||||||||||||||||| || ||||| ||||| ||||||||||||||||||||||||||| ||||||||||| | | |             |  | | ||||   | |      || |||||||  | |   || |  ||   |  ||   |  || |  | || ||  |     ||| ||| | | |||||
ACTTACAGAAGCTGGGAGTGATCGTGTAATTGTATGTGATATTCATTCCACTCAAGCATTGGGATACTTCGATATTCCTGTGGATCATATACATGGACAGgtactcttaacagaccaagatatgttccttttattacctaaatgctgttttcagttgtacgcaattttcttagctggatctgagttggcagcaaagtaacgattgaatctttgttatatgtag

upper sequence: GRMZM2G180863_T01 (Zea mays), 5'ss of exon 4
lower sequence: EFJ24123 (Selaginella moellendorffii), 5'ss of exon 4

ACTTACTGAAGCTGGTAGTGACCGTGTCATTGTATGTGATATTCATTCTACGCAAGCGTTGGGGTACTTCGATATTCCTGTGGATCATATATATGGACAGgtagtgtgagttct-tcctttacagcgtt-tgatttcagtattgcatctcgttgtaaattctatctgactacgaattagtgtcatccttggtgtctgtag
  | ||||| || |||    | |||||  |||  |||||| |||| |||   |||    |||||||||||||||||||||| |||||  | |||||||||||| |||| ||  | |  ||  || |||    ||| | ||||   ||||| |||    ||||  | |                                 
TATAACTGAGGCAGGTGCAAATCGTGTTCTTGCGTGTGATCTTCACTCTGGACAAAGTATGGGGTACTTCGATATTCCTGTTGATCACGTCTATGGACAGgta-tgtgcgtcatatttttctcaacgtcaccattcccgtataaaatctctttgctctttcttgcag---------------------------------

upper sequence: GRMZM2G180863_T01 (Zea mays), 5'ss of exon 4
lower sequence: EFJ35181 (Selaginella moellendorffii), 5'ss of exon 4

ACTTACTGAAGCTGGTAGTGACCGTGTCATTGTATGTGATATTCATTCTACGCAAGCGTTGGGGTACTTCGATATTCCTGTGGATCATATATATGGACAGgtagtgtgagttct-tcctttacagcgtt-tgatttcagtattgca-tctcgttgtaaattctatctgactacgaattagtgtcatccttggtgtctgtag
  | ||||| || |||    | |||||  |||  |||||  |||| |||   |||    |||||||||||||||||||||| |||||  | |||||||||||| |||| ||  | |  ||  || |||    ||| | |||    | |||| |||    ||||  | |                                 
TATAACTGAGGCAGGTGCAAATCGTGTTCTTGCGTGTGACCTTCACTCTGGACAAAGTATGGGGTACTTCGATATTCCTGTTGATCACGTCTATGGACAGgta-tgtgcgtcatatttttctcaacgtcaccattcccgtacaaaaatctctttgctctttcttgcag---------------------------------

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|149088668|gb|EE177786.2|EE177786

EST:     CGCAAGCGTTGGGGTACTTCGATATTCCTGTGGATCATATATATGGACAG                         CCTGTGATTCTGGATTACCTGGCCAGCAAGACGATATCTGAAGATCTTGTG
genomic: CGCAAGCGTTGGGGTACTTCGATATTCCTGTGGATCATATATATGGACAGgtagtgtgag ... gtgtctgtagCCTGTGATTCTGGATTACCTGGCCAGCAAGACGATATCTGAAGATCTTGTG

EST: gi|78088529|gb|DV516922.1|DV516922

EST:     CGCAAGCGTTGGGGTACTTCGATATTCCTGTGGATCATATATATGGACAG                         CCTGTGATTCTGGATTACCTGGCCA
genomic: CGCAAGCGTTGGGGTACTTCGATATTCCTGTGGATCATATATATGGACAGgtagtgtgag ... gtgtctgtagCCTGTGATTCTGGATTACCTGGCCA

EST: gi|149112871|gb|EE191452.2|EE191452

EST:     CGCAAGCGTTGGGGTACTTCGATATTCCTGTGGATCATATATATGGACAG                         CCTGTGATTCTGGATTACC
genomic: CGCAAGCGTTGGGGTACTTCGATATTCCTGTGGATCATATATATGGACAGgtagtgtgag ... gtgtctgtagCCTGTGATTCTGGATTACC

EST: gi|6626351|gb|AW257883.1|AW257883

EST:     CACAAGCGTTGGGGTACTTCGATATTCCTGTGGATCATATATATGGACAG                         CCTGTGATTCTGGATTACCTGGCCAGCAAGACGATATCTGAAGATCTTGTG
genomic: CGCAAGCGTTGGGGTACTTCGATATTCCTGTGGATCATATATATGGACAGgtagtgtgag ... gtgtctgtagCCTGTGATTCTGGATTACCTGGCCAGCAAGACGATATCTGAAGATCTTGTG

EST: gi|74240297|gb|DT648211.1|DT648211

EST:     CGCAAGCGTTGGGGTACTTCGATATTCCTGTGGATCATATATATGGACAG                         CCTGTGATTCTGGATTACCTGGCCAGCAAGACGATATCTGAAGATCTTGTG
genomic: CGCAAGCGTTGGGGTACTTCGATATTCCTGTGGATCATATATATGGACAGgtagtgtgag ... gtgtctgtagCCTGTGATTCTGGATTACCTGGCCAGCAAGACGATATCTGAAGATCTTGTG

EST: gi|149006976|gb|EE040195.2|EE040195

EST:     CGCAAGCGTTGGGGTACTTCGATATTCCTGTGGATCATATATATGGACAG                         CCTGTGATTCTGGATTACCTGGCCAGCA
genomic: CGCAAGCGTTGGGGTACTTCGATATTCCTGTGGATCATATATATGGACAGgtagtgtgag ... gtgtctgtagCCTGTGATTCTGGATTACCTGGCCAGCA

EST: gi|71770134|gb|DR968071.1|DR968071

EST:     CGCAAGCGTTGGGGTACTTCGATATTCCTGTGGATCATATATATGGACAG                         CCTGTGATTCTGGATTACCTGGCCAGCAAG
genomic: CGCAAGCGTTGGGGTACTTCGATATTCCTGTGGATCATATATATGGACAGgtagtgtgag ... gtgtctgtagCCTGTGATTCTGGATTACCTGGCCAGCAAG

EST: gi|31354391|gb|CD438748.1|CD438748

EST:     CGCAAGCGTTGGGGTACTTCGATATTCCTGTGGATCATATATATGGACAG                         CCTGTGATTCTGGATTACCTGGCCAGCAAGACGATATCTGAAGATCTTGTG
genomic: CGCAAGCGTTGGGGTACTTCGATATTCCTGTGGATCATATATATGGACAGgtagtgtgag ... gtgtctgtagCCTGTGATTCTGGATTACCTGGCCAGCAAGACGATATCTGAAGATCTTGTG

EST: gi|149000114|gb|EE037239.2|EE037239

EST:     CGCAAGCGTTGGGGTACTTCGATATTCCTGTGGATCATATATATGGACAG                         CCTGTGATTCTGAATTACCTGGCCAGCAAGACGATATCTGAAGATCTTGTG
genomic: CGCAAGCGTTGGGGTACTTCGATATTCCTGTGGATCATATATATGGACAGgtagtgtgag ... gtgtctgtagCCTGTGATTCTGGATTACCTGGCCAGCAAGACGATATCTGAAGATCTTGTG

EST: gi|149079724|gb|EE168725.2|EE168725

EST:     CGCAAGCGTTGGGGTACTTCGATATTCCTGTGGATCATATATATGGACAG                         CCTGTGATTCTGGATTACCTGGCCAGCA
genomic: CGCAAGCGTTGGGGTACTTCGATATTCCTGTGGATCATATATATGGACAGgtagtgtgag ... gtgtctgtagCCTGTGATTCTGGATTACCTGGCCAGCA

EST: gi|50322471|gb|CO517597.1|CO517597

EST:     CGCAAGCGTTGGGGTACTTCGATATTCCTGTGGATCATATATATGGACAG                         CCTGTGATTCTGGATTACCTGGCCAGCAAGACGATATCTGAAGATCTTGTG
genomic: CGCAAGCGTTGGGGTACTTCGATATTCCTGTGGATCATATATATGGACAGgtagtgtgag ... gtgtctgtagCCTGTGATTCTGGATTACCTGGCCAGCAAGACGATATCTGAAGATCTTGTG

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), 49 (downstream exon)
Score: 140

ACTTACTGAAGCTGGTAGTGACCGTGTCATTGTATGTGATATTCATTCTACGCAAGCGTTGGGGTACTTCGATATTCCTGTGGATCATATATATGGACAGgtagtgtgag ... gtgtctgtagCCTGTGATTCTGGATTACCTGGCCAGCAAGACGATATCTGAAGATCTTGTGGTTGTTTCTCCTGATGTGGGTGGCGTTGTTAGAGCACGTGCATTCGCTA

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 316

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 185