ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
PPT, BS, UA-tract

Sequence

atgc intronic sequence ATGC exonic sequence

gtaatcttaaatatacaactcctcacatgatatgtgggtaatgatacaggtataactgtgcctttgcttacagcattctttttatgcatttccagGAAAGCCAGTGTACATGTATAGTATGGGTGGGCTTGCAGAATATTGCGTTGTGCCAGCCAACGCACTAGCAGTTCTTCCCAACTCTTTGCCATACACAGA

Basic information

species	Oryza sativa
transcript	LOC_Os08g01760.1
intron #	4
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: LOC_Os08g01760.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G024303_T01 (Zea mays), 3'ss of exon 4

--------------gtaatcttaaatatacaactcctcacatgatatgtgggtaatgatac------aggtataactgtgcctttgcttacagcattcttt---ttatgcatttccagGAAAGCCAGTGTACATGTATAGTATGGGTGGGCTTGCAGAATATTGCGTTGTGCCAGCCAACGCACTAGCAGTTCTTCCCAACTCTTTGCCATACACAGA
                 |||   |  || || |  |     | | |     ||| |  |            |  || ||    ||||||  || |  ||     || | ||| | |||| || || |||||||||||||||||||| ||||||||||| ||||| ||||| |||||||| || ||||||||||| ||  ||||  |||||||||||||
gtaacctgaggaaacagatccacatcatgcatcatcatcagtaacaccacagtattttttttaccgagaacaccacagtataattgcttcaagtaacctgaaaattctccatctgcagGGAAACCGGTGTACATGTATAGTATGGGAGGGCTTGCAGAGTATTGTGTTGTCCCAGCCAATGCGCTAGCAGTTCTCCCTGACTCACTGCCATACACAGA

upper sequence: LOC_Os08g01760.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G135526_T01 (Zea mays), 3'ss of exon 4

gtaatcttaaatatacaactcct----cacatgatatgtgggtaat-gat-acaggtataactgtgcctttgcttac--agcattctttttatgcatttccagGAAAGCCAGTGTACATGTATAGTATGGGTGGGCTTGCAGAATATTGCGTTGTGCCAGCCAACGCACTAGCAGTTCTTCCCAACTCTTTGCCATACACAGA
|||| |  |     |  |  | |    | ||| |     |   ||| |||  | ||    ||   ||| |     ||  ||||| ||     |||   | |||| ||||| ||||||||||| || ||||| || ||||| || || ||||| |||||||||||||| || || || || |||  |||  |||| ||||| ||
gtaaacacacccgcatcatgcatgtcacgcatcactgcagcacaatcgatcgccggacgcaccaggccctgaaaaactaagcatcctccgcctgc---ttcagGGAAGCCGGTGTACATGTACAGCATGGGAGGCCTTGCGGAGTACTGCGTGGTGCCAGCCAACGCGCTGGCGGTCCTCCCCGCCTCGCTGCCGTACACGGA

upper sequence: LOC_Os08g01760.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA08G00740.2 (Glycine max), 3'ss of exon 5

-gtaatcttaaatatacaactcctcacatg-atatgtgggtaatgata----caggtataactgtgcctttgcttacagcattctttttatgcatttccagGAAAGCCAGTGTACATGTATAGTATGGGTGGGCTTGCAGAATATTGCGTTGTGCCAGCCAACGCACTAGCAGTTCTTCCCAACTCTTTGCCATACACAGA
  || |   || |  |    || |||  || || | |   |||| ||     ||   || | ||    ||||   |    |     |||    ||||  |||||| ||||  ||||||||||||||||| |||||||| ||||| || ||||||||||| || | | |  | ||  | ||  |||| |||||||| |||||
gctagtacaaatttcaatgttcttcaagtgcatttatccctaattatgggatcattcattattgaaaatttggaaaactgaaaaagtttgca-atttatagGAAAACCAGCATACATGTATAGTATGGGAGGGCTTGCTGAATACTGTGTTGTGCCAGCAAATGGAGTGTCTGTGTTACCAGACTCATTGCCATATACAGA

upper sequence: LOC_Os08g01760.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA05G33140.1 (Glycine max), 3'ss of exon 4

gtaatcttaaatatacaactcctcacatg-atatgtgggtaatgata----caggtataactgtgc--ctttgcttacagcattctttttatgcatttccagGAAAGCCAGTGTACATGTATAGTATGGGTGGGCTTGCAGAATATTGCGTTGTGCCAGCCAACGCACTAGCAGTTCTTCCCAACTCTTTGCCATACACAGA
 || |    | |  |    || |||  || || | |   ||||  |     ||   || | ||      || |  ||| | |     |||    | || ||||||| ||||  | ||||||||||||||| |||||||| ||||| |||||||||||||| || | | |  | ||  | ||  |||| |||||||| |||||
-tagtacatatttcaatgttcttcaagtgcatttatccctaattgtgggatcattcattattggaaaatttggaatactgaaaaaagtttgc-tacttacagGAAAACCAGCATTCATGTATAGTATGGGAGGGCTTGCTGAATACTGCGTTGTGCCAGCAAATGGAGTGTCTGTATTACCAGACTCATTGCCATATACAGA

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|58597603|gb|CK008131.1|CK008131

EST:     ATTATTCCTTCGTAGCAATG                         GAAAGCCAGTGTACATGTATAGTCTGGGTGGGCTATGCAGAATATTGCGTT
genomic: ATTATTCCTTCGTAGCAATGgtaatcttaa ... gcatttccagGAAAGCCAGTGTACATGTATAGTATGGGTGGGCT-TGCAGAATATTGCGTT

EST: gi|2312625|gb|C28780.1|C28780

EST:     TAAAGGAACGCTATACGATGGTCAAACCCGATTATTCCTTCGTAGCAATG                         GAAAGCCAGTGTACATGTATAGTATGGGTGGGCTTGCAGAATATTGCGTTG
genomic: TAAAGGAACGCTATACGATGGTCAAACCCGATTATTCCTTCGTAGCAATGgtaatcttaa ... gcatttccagGAAAGCCAGTGTACATGTATAGTATGGGTGGGCTTGCAGAATATTGCGTTG

EST: gi|44674419|gb|CR287853.1|CR287853

EST:     TAAAGGAACGCTATACGATGGTCAAACCCGATTATTCCTTCGTAGCAATG                         GAAAGCCAGTGTACATGTATAGTATGGGTGGGCTTGCAGAATATTGCGTTG
genomic: TAAAGGAACGCTATACGATGGTCAAACCCGATTATTCCTTCGTAGCAATGgtaatcttaa ... gcatttccagGAAAGCCAGTGTACATGTATAGTATGGGTGGGCTTGCAGAATATTGCGTTG

EST: gi|7593811|gb|AU065734.2|AU065734

EST:     TAAAGGAACGCTATACGATGGTCAAACCCGATTATTCCTTCGTAGCAATG                         GAAAGCCAGTGTACATGTATAAGTATGG
genomic: TAAAGGAACGCTATACGATGGTCAAACCCGATTATTCCTTCGTAGCAATGgtaatcttaa ... gcatttccagGAAAGCCAGTGTACATGTATA-GTATGG

EST: gi|66916958|gb|CX103806.1|CX103806

EST:     TAAAGGAACGCTATACGATGGTCAAACCCGATTATTCCTTCGTAGCAATG                         GAAAGCCAGTGTACATGTATAGTATGGGTGGGCTTGCAGAATATTGCGTTG
genomic: TAAAGGAACGCTATACGATGGTCAAACCCGATTATTCCTTCGTAGCAATGgtaatcttaa ... gcatttccagGAAAGCCAGTGTACATGTATAGTATGGGTGGGCTTGCAGAATATTGCGTTG

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 1 RNA-Seqlibrary.

Block sizes: 75 (upstream exon), 63 (downstream exon)
Score: 35

GGCCAAGAAGATCTGTGTGAGTCTTTCTTTGCATACAACCGTGCTAAAGGAACGCTATACGATGGTCAAACCCGATTATTCCTTCGTAGCAATGgtaatcttaa ... gcatttccagGAAAGCCAGTGTACATGTATAGTATGGGTGGGCTTGCAGAATATTGCGTTGTGCCAGCCAACGCACTAGCAGTTCTTCCCAACTCTTTGCCATACACAGA

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atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

atgatacaggtataactgtgcctttgcttacagcattctttttatgcatttccagGAAAGCCAGTGTACATGTATAGTATGGGTGGGCTTGCAGAATATTGCGTTGTGCCAGCCAACGCACTAGCAGTTCTTCCCAACTCTTTGCCATACACAGA