ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtactaactgcaaaccattagttgtggtcctgtataatgctcttatgcatgtacatccttttgatgtatatccttggataatatttttgatgtgattttgaggattgtttctagctatgatcactctccttttcctaaacatgcgttgaagttgtgagtctaatttaacagatcaatttggaaatttgcagATGGAGAAAAGCGCAGTTCTTTACAGGCCAAAATTGATAGTAGCTGGTGCCAGTGCCTATGCTCGCCATTACGACTATGCTCGTATGCGCAAG

Basic information

species	Physcomitrella patens
transcript	PP1S79_54V6.1
intron #	7
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: PP1S79_54V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: LOC_Os03g52840.2 (Oryza sativa), 3'ss of exon 7

gtactaactgcaaaccattagttgtggtcctgtataatgctcttatgcatgtacatccttttgatgtatatccttggataatatttttgatgtgattttgaggattgtttctagctatgatcactctccttttcctaaacatgcgttgaagttgtgagtctaatttaaca-gatcaatttggaaattt---gcagATGGAGAAAAGCGCAGTTCTTTACAGGCCAAAATTGATAGTAGCTGGTGCCAGTGCCTATGCTCGCCATTACGACTATGCTCGTATGCGCAAG
                                                                                            | || | |   ||| ||  | ||  | ||  ||||     |  | ||  |   |  |  |   || | |    | ||| | |  |||||  | ||     |||||||||||||| || |||||||  |||||||| ||||| || || ||||| ||||| ||||| || | ||| |||||||  || ||||| |||
-------------------------------------------------------------------------------------------attatctaggatatttttcattgcc-tcatatctctttcaattgtgaaattatttcaagat---gaatttctgctgacatgcttgatttgctacttctgcacagATGGAGAAAAGTGCCGTTCTTTTTAGGCCAAAGTTGATCGTTGCGGGTGCAAGTGCATATGCGCGTCTTTATGACTATGACCGCATGCGGAAG

upper sequence: PP1S79_54V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GRMZM2G135283_T02 (Zea mays), 3'ss of exon 7

gtactaactgcaaaccattagttgtggtcctgtataatgctcttatgcatgtacatccttttgatgtatatccttggataatatttttgatgtgattttgaggattgtttctagctatgatcactctccttttcctaaacatgcgttgaagttgtgagtctaatttaacagatcaatt--tggaaatttgcagATGGAGAAAAGCGCAGTTCTTTACAGGCCAAAATTGATAGTAGCTGGTGCCAGTGCCTATGCTCGCCATTACGACTATGCTCGTATGCGCAAG-------
                                                                                         || ||    ||    || | | |   |||| | |   |  |||      |    |  | |     |   |    |   |    ||| ||  |    || |  || ||||||||||||| |||||||  |||||||| |||||  | |||||||| ||||| |||||||| |  || || ||||  |||||||| |||       
-----------------------------------------------------------------------------------------atttgtcactgtcatttctctttg--tatggtaaacatattttgagatgaatcacactaacaccttactttc--tcctatgcttcatttgctacctatgtatagTTGGAGAAAAGCGCTGTTCTTTTTAGGCCAAAGTTGATCATTGCTGGTGCAAGTGCATATGCTCGGCTATATGATTATGACCGTATGCGGAAGGCAAGGT

upper sequence: PP1S79_54V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GRMZM2G135283_T03 (Zea mays), 3'ss of exon 7

gtactaactgcaaaccattagttgtggtcctgtataatgctcttatgcatgtacatccttttgatgtatatccttggataatatttttgatgtgattttgaggattgtttctagctatgatcactctccttttcctaaacatgcgttgaagttgtgagtctaatttaacagatcaatt--tggaaatttgcagATGGAGAAAAGCGCAGTTCTTTACAGGCCAAAATTGATAGTAGCTGGTGCCAGTGCCTATGCTCGCCATTACGACTATGCTCGTATGCGCAAG
                                                                                         || ||    ||    || | | |   |||| | |   |  |||      |    |  | |     |   |    |   |    ||| ||  |    || |  || ||||||||||||| |||||||  |||||||| |||||  | |||||||| ||||| |||||||| |  || || ||||  |||||||| |||
-----------------------------------------------------------------------------------------atttgtcactgtcatttctctttg--tatggtaaacatattttgagatgaatcacactaacaccttactttc--tcctatgcttcatttgctacctatgtatagTTGGAGAAAAGCGCTGTTCTTTTTAGGCCAAAGTTGATCATTGCTGGTGCAAGTGCATATGCTCGGCTATATGATTATGACCGTATGCGGAAG

upper sequence: PP1S79_54V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA02G38160.2 (Glycine max), 3'ss of exon 7

gtactaactgcaaaccattagttgtggtcctgtataatgctcttatgcatgtacatccttttgatgtatatccttggataatatttttgatgtgattttgaggattgtttctagctatgatcactctccttttcctaaacatgcgttgaagttgtgagtctaatttaacagatcaatttg---gaaatttgcagATGGAGAAAAGCGCAGTTCTTTACAGGCCAAAATTGATAGTAGCTGGTGCCAGTGCCTATGCTCGCCATTACGACTATGCTCGTATGCGCAAG
                                                                                        |||| |   || ||  |      ||  |   |  | || || |||| |  | |   ||||  |||| || | |  | ||| || |  | ||     | ||| |||| |||||||||| ||||| ||||  ||||||||||| ||||| |||||||| ||||| |||||||||| ||| || ||||| ||| | ||||||
----------------------------------------------------------------------------------------gatgaggggtt-agattcacacttatttgcaa--agtccccctttcatgcatac-tgttg--gttgagactgttctataatagcttgacttatttaatattcgcagTTGGAGAAAAGTGCAGTACTTTTTAGGCCAAAATTAATAGTTGCTGGTGCTAGTGCTTATGCTCGCCTTTATGATTATGCACGTGTTCGCAAG

upper sequence: PP1S79_54V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA14G36280.1 (Glycine max), 3'ss of exon 7

gtactaactgcaaaccattagttgtggtcctgtataatgctcttatgcatgtacatccttttgatgtatatccttggataatatttttgatgtgattttgaggattgtttctagctatgatcactctccttttcctaaacatgcgttgaagttgtgagtctaatttaacagatcaatttg---gaaatttgcagATGGAGAAAAGCGCAGTTCTTTACAGGCCAAAATTGATAGTAGCTGGTGCCAGTGCCTATGCTCGCCATTACGACTATGCTCGTATGCGCAAG
                                                                                          ||||||   | || | | |||   || ||   | || || |||| |  | |   ||||  |||| || | |  | |||  | |  | ||     | ||  |||| |||||||||| ||||  ||||  ||||||||||| ||||| |||||||| ||||| |||||||||| ||| || ||||| ||| | ||||||
------------------------------------------------------------------------------------------tgtgatga-ggggttagattcacactttgcaaagtccccctttcatgcatac-tgttg--gttgagactttcctataattgcttgacttatttaatatccgcagTTGGAGAAAAGTGCAGCACTTTTTAGGCCAAAATTAATAGTTGCTGGTGCTAGTGCTTATGCTCGCCTTTATGATTATGCACGTGTTCGCAAG

upper sequence: PP1S79_54V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: AT4G37930.1 (Arabidopsis thaliana), 3'ss of exon 7

gtactaactgcaaaccattagttgtggtcctgtataatgctcttatgcatgtacatccttttgatgtatatccttggataatatttttgatgtgattttgaggattgtttctagctatgatcactctccttttcctaaacatgcgttgaagttgtgagtctaatttaacagatcaatttggaaatttgcagATGGAGAAAAGCGCAGTTCTTTACAGGCCAAAATTGATAGTAGCTGGTGCCAGTGCCTATGCTCGCCATTACGACTATGCTCGTATGCGCAAG
                                                                                             | | || |   || | |  ||| || || | |  | | |  |||| |  || |   |    |       |  |||    | ||||| ||  |||||||||||||||||| ||   ||||| ||||||||||||||| || |||||||| ||||| |||||| |    || |||||||| || ||  | |||
---------------------------------------------------------------------------------------------gttcttaactcttctattaagcaatcat-agtaacttataactaacc-cgcttcataacaat-------acataagtctttaattttga--tttgcagATGGAGAAAAGTGCTACTCTTTTCAGGCCAAAATTGATTGTTGCTGGTGCAAGTGCTTATGCTAGATTGTATGACTATGCCCGCATCAGAAAG

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|162182305|gb|FC357176.1|FC357176

EST:     CTATGCCATACCGATTGGACGAGTCTACAGGTTACATAGACTACGATACG                         ATGGAGAANAGCGCAGTTCTTTACAGGCCAAAATTGATAGTAGCTGGTGCC
genomic: CTATGCCATACCGATTGGACGAGTCTACAGGTTACATAGACTACGATACGgtactaactg ... aaatttgcagATGGAGAAAAGCGCAGTTCTTTACAGGCCAAAATTGATAGTAGCTGGTGCC

EST: gi|100385980|gb|BY951174.1|BY951174

EST:     CTATGCCATACCGATTGGACGAGTCTACAGGTTACATAGACTACGATACG                         ATGGAGAAAAGCGCAGTTCTTTACAGGCCAAAATTGATAGTAGCTGGTGCC
genomic: CTATGCCATACCGATTGGACGAGTCTACAGGTTACATAGACTACGATACGgtactaactg ... aaatttgcagATGGAGAAAAGCGCAGTTCTTTACAGGCCAAAATTGATAGTAGCTGGTGCC

EST: gi|208379665|gb|DC903720.1|DC903720

EST:     CTATGCCATACCGATTGGACGAGTCTACAGGTTACATAGACTACGATACG                         ATGGAGAAAAGCGCAGTTCTT-ACAGGC-AAAATNGATAG
genomic: CTATGCCATACCGATTGGACGAGTCTACAGGTTACATAGACTACGATACGgtactaactg ... aaatttgcagATGGAGAAAAGCGCAGTTCTTTACAGGCCAAAATTGATAG

EST: gi|162155361|gb|FC331767.1|FC331767

EST:     CTATGCCATACCGATTGGACGAGTCTACAGGTTACATAGACTACGATACG                         ATGGAGAANAGCGCAGTTCTTTACAGGCCAAAATTGATAGTAGCTGGTGCC
genomic: CTATGCCATACCGATTGGACGAGTCTACAGGTTACATAGACTACGATACGgtactaactg ... aaatttgcagATGGAGAAAAGCGCAGTTCTTTACAGGCCAAAATTGATAGTAGCTGGTGCC

EST: gi|100392460|gb|BY953374.1|BY953374

EST:     TATGCCATACCGAT-GGNACGAGTCTACAGGTTACATAGACTACGATACG                         ATGGAGAAAAGCGCAGTTCTTTTACAGGC-AAAATTGAT
genomic: TATGCCATACCGATTGG-ACGAGTCTACAGGTTACATAGACTACGATACGgtactaactg ... aaatttgcagATGGAGAAAAGCGCAGTTCTTT-ACAGGCCAAAATTGAT

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: 26 (upstream exon), 30 (downstream exon)
Score: 2

ACGGACATGAAGAAAATCTCGGCGGTTTCCATTTTCTTCGAGACTATGCCATACCGATTGGACGAGTCTACAGGTTACATAGACTACGATACGgtactaactg ... aaatttgcagATGGAGAAAAGCGCAGTTCTTTACAGGCCAAAATTGATAGTAGCTGGTGCCAGTGCCTATGCTCGCCATTACGACTATGCTCGTATGCGCAAG

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atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

aaacatgcgttgaagttgtgagtctaatttaacagatcaatttggaaatttgcagATGGAGAAAAGCGCAGTTCTTTACAGGCCAAAATTGATAGTAGCTGGTGCCAGTGCCTATGCTCGCCATTACGACTATGCTCGTATGCGCAAG