ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtacttgacaaagccttgcaatgtggcgatgtaccaaaatacgttttgaagttggagtcaatagtctgccaatctggattcaattcgtagaggctttacgttcatgcacgtgatatctgaggatgctgagttgatgccatttgttgatcatgtccttgttaacttggaggatggggttttgtgcagGGCCAATGCGCAACAGCCCAAGCTGTTTGTAGGAATGATCCTGATTCTGATTTTCGCCGAGGCGCTGGCTTTATACGGACTTATCGTGGGTATCATTCTG

Basic information

species	Physcomitrella patens
transcript	PP1S200_79V6.1
intron #	2
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: PP1S200_79V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G177005_T01 (Zea mays), 3'ss of exon 2

gtacttgacaaagccttgcaatgtggcgatgtaccaaaatacgttttgaagttggagtcaatagtctgccaatctggattcaattcgtagaggctttacgttcatgcacgtgatatctgaggatgctgagttgatgccatttgttgatcatgtccttgttaacttggaggatggggttttgtgcagGGCCAATGCGCAACAGCCCAAGCTGTTTGTAGGAATGATCCTGATTCTGATTTTCGCCGAGGCGCTGGCTTTATACGGACTTATCGTGGGTATCATTCTG
                                                                      |      || ||| |        | |  ||||  | |   |     | ||||| ||       |||  | |||   ||  |    |   ||| ||   ||     | |||   |||||| |||||||||||||| ||||| || || || |||||||| || || |||||||| || ||||| ||| | || || || || || || || || || 
-------------------------------------------------------------------agtagctcacatgcaactttct----cctggcgtttcttctttta----cagaggaggc-------atgggaattga-aattttagtttgactaatttttgggccaccgattt---cagGGCAAATGCGCAACAGCCAAAGCTTTTCGTTGGCATGATCCTCATCCTCATTTTCGCAGAAGCGCTTGCTCTCTATGGTCTAATTGTTGGAATTATCCTT

upper sequence: PP1S200_79V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT1G75630.1 (Arabidopsis thaliana), 3'ss of exon 2

gtacttgacaaagccttgcaatgtggcgatgtaccaaaatacgttttgaagttggagtcaatagtctgccaatctggattcaattcgtagaggctttacgttcatgcacgtgatatctgaggatgctgagttgatgccatttgttgatcatgtccttgttaacttggaggatggggttttgtgcagGGCCAATGCGCAACAGCCCAAGCTGTTTGTAGGAATGATCCTGATTCTGATTTTCGCCGAGGCGCTGGCTTTATACGGACTTATCGTGGGTATCATTCTG
                                                                       |   |  ||  |   |   | |||||   ||| |  || | |  | |        || |       ||||    || |      |||||||  |  |   ||   | || ||||| || ||||||||||| || ||||||||||| |||||||| |||||||| || || || || ||||| ||  | || || || || || |||||||| || 
-----------------------------------------------------------------------acaggcgttgcacctg---atgctttgttttcttttacatcaactata-------tgtgacagcatcattca--gaactctgttttgttaatctcaa---tgtcttattttgcagAGCGAATGCGCAACAACCGAAGCTGTTTGTGGGAATGATTCTGATTCTCATCTTTGCGGAAGCGCTTGCACTGTATGGTCTCATTGTTGGTATCATCCTC

upper sequence: PP1S200_79V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT1G75630.2 (Arabidopsis thaliana), 3'ss of exon 3

------gtacttgaca--aagccttgcaatg-tggcgatgtaccaaaat--acgttttgaagttggagtcaatagtctgccaatctggattcaattcgtagag-gctttacgttcatgcacgtgatatctgaggatgctgagttgatgccatttgttgatcatgtccttgttaacttggaggatggggttttgtgcagGGCCAATGCGCAACAGCCCAAGCTGTTTGTAGGAATGATCCTGATTCTGATTTTCGCCGAGGCGCTGGCTTTATACGGACTTATCGTGGGTATCATTCTG
       |  |||| |  |    | |   || |   ||  |  |   ||  |   |||||||  |      |||   | ||| |  | ||||||   |    |  | | | | |        |  ||  | |      || |       ||||    || |      |||||||  |  |   ||   | || ||||| || ||||||||||| || ||||||||||| |||||||| |||||||| || || || || ||||| ||  | || || || || || |||||||| || 
gtaacgttgtttgatattagatttggtgttggttaagaactgtctggattgaatctttgaagcagattaggataaattaccagta-gaattcaacaggcgttgcacctgatgctttgttttcttttacatcaactatatgtgacagcatcattca--gaactctgttttgttaatctcaa---tgtcttattttgcagAGCGAATGCGCAACAACCGAAGCTGTTTGTGGGAATGATTCTGATTCTCATCTTTGCGGAAGCGCTTGCACTGTATGGTCTCATTGTTGGTATCATCCTC

upper sequence: PP1S200_79V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EDP08338 (Chlamydomonas reinhardtii), 3'ss of exon 3

gtacttgacaaagccttgcaatgtggcgatgtaccaaaatacgttttgaagttggagtcaatagtctgccaatctggattcaattcgtagaggctttacgttcatgcacgtgatatctgagg-atgctgagttgatgccatttgttgatcatgtccttgttaacttggaggatggggttttgtgcagGGCCAATGCGCAACAGCCCAAGCTGTTTGTAGGAATGATCCTGATTCTGATTTTCGCCGAGGCGCTGGCTTTATACGGACTTATCGTGGGTATCATTCTG
                                                                                                || ||  | |||   |   ||| ||| ||  |  ||| |    |||      || | | | ||    ||||                 ||| || || || || || ||||||||||| || || ||||| ||||||||||||||||| |||||||| ||| | ||||| || || |              
-----------------------------------------------------------------------------------------------gtaagtctacgca---gccttctcaggcattttaggttcagagtattaaccagtccttttcctg---gcttg-----------------cagCGCTAACGCCCAGCAACCCAAGCTGTTCGTCGGTATGATTCTGATTCTGATTTTCGCTGAGGCGCTCGCTCTTTACGGCCTGATTG--------------

upper sequence: PP1S200_79V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ14420 (Selaginella moellendorffii), 3'ss of exon 2

gtacttgacaaagccttgcaatgtggcgatgtaccaaaatacgttttgaagttggagtcaatagtctgccaatctggattcaattcgtagaggctttacgttcatgcacgtgatatctgaggatgctgagttgatgccatttgttgatcatgtccttgttaacttggaggatggggttttgtgcagGGCCAATGCGCAACAGCCCAAGCTGTTTGTAGGAATGATCCTGATTCTGATTTTCGCCGAGGCGCTGGCTTTATACGGACTTATCGTGGGTATCATTCTG
                                                                                                             || |  ||    ||| |  |    ||    ||  | |||    ||    || | |    |  ||   || | |||||||| |||||||| || |||||||| ||||| ||||||||||| ||||| || || ||||||||  ||||| ||||||| || || ||||| ||||| |||
-------------------------------------------------------------------------------------------------------------gtaagttcgatcgat-caaaagccatctttttcttcgat---atctccattgatt---ggtttgtttttctttgcagGGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTCATTCTCATCTTTGCCGAGGCTTTGGCTCTATACGGTCTCATTGTGGGAATCATCCTG

upper sequence: PP1S200_79V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ37480 (Selaginella moellendorffii), 3'ss of exon 2

gtacttgacaaagccttgcaatgtggcgatgtaccaaaatacgttttgaagttggagtcaatagtctgccaatctggattcaattcgtagaggctttacgttcatgcacgtgatatctgag-gatgctgagttgatgccatttgttgatcatgtccttgttaacttggaggatggggttttgtgcagGGCCAATGCGCAACAGCCCAAGCTGTTTGTAGGAATGATCCTGATTCTGATTTTCGCCGAGGCGCTGGCTTTATACGGACTTATCGTGGGTATCATTCTG
                                                                                  ||| | |||  |   |  ||  | | |   | || |    | ||   | |  |  |  |||  |  || || | || | |  ||  |   |      ||   ||||||||| || |||||||| ||||| || || || |||||| |||| || || |||||||||||||||||| | |||||| | |||||||| |||||||| 
-------------------------------------------------------------------------------atcatttgaagat-cgcgagcttggtcctcacaagatttccctgctggaaactccactctgttttcttctc-tggctttctcactttccatcgt------tttcacagGGCCAACGCTCAACAGCCAAAGCTCTTCGTGGGCATGATCTTGATCCTCATCTTCGCCGAGGCGCTGGCTCTCTACGGATTGATCGTGGGGATCATTCTT

upper sequence: PP1S200_79V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ33972 (Selaginella moellendorffii), 3'ss of exon 2

gtacttgacaaagccttgcaatgtggcgatgtaccaaaatacgttttgaagttggagtcaatagtctgccaatctggattcaattcgtagaggctttacgttcatgcacgtgatatctgaggatgctgagttgatgccatttgttgatcatgtccttgttaacttggaggatggggttttgtgcagGGCCAATGCGCAACAGCCCAAGCTGTTTGTAGGAATGATCCTGATTCTGATTTTCGCCGAGGCGCTGGCTTTATACGGACTTATCGTGGGTATCATTCTG
                                                                       |||   |||  |      |  ||||     ||    ||  ||| ||   |  ||   | |  |  |  |||  |  || || | || | |  ||  |   |      ||   ||||||||| || |||||||| ||||| || || || |||||| |||| || || |||||||||||||||||| | |||||| | |||||||| |||||||| 
-----------------------------------------------------------------------atc---atttgaagatcgggagcttggtcctc----acaagatttccctgc-tggaaactccactctgttttcttctc-tggctttctcactttccatcgt------tttcacagGGCCAACGCTCAACAGCCAAAGCTCTTCGTGGGCATGATCTTGATCCTCATCTTCGCCGAGGCGCTGGCTCTCTACGGATTGATCGTGGGGATCATTCTT

upper sequence: PP1S200_79V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ26016 (Selaginella moellendorffii), 3'ss of exon 2

gtacttgacaaagccttgcaatgtggcgatgtaccaaaatacgttttgaagttggagtcaatagtctgccaatctggattcaattcgtagaggctttacgttcatgcacgtgatatctgaggatgctgagttgatgccatttgttgatcatgtccttgttaacttggaggatggggttttgtgcagGGCCAATGCGCAACAGCCCAAGCTGTTTGTAGGAATGATCCTGATTCTGATTTTCGCCGAGGCGCTGGCTTTATACGGACTTATCGTGGGTATCATTCTG
                                                                                                             || |  ||    ||| |  |    ||    ||  | |||    ||    || | |    |  ||   || | |||||||| |||||||| || |||||||| ||||| ||||||||||||||||| || || ||||||||  ||||| ||||||| || || ||||| ||||| |||
-------------------------------------------------------------------------------------------------------------gtaagttcgatcgat-caaaaaccatctttttcttcgat---atctccattgatt---ggtttgtttttctttgcagGGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTGATTCTCATCTTTGCCGAGGCTTTGGCTCTATACGGTCTCATTGTGGGAATCATCCTG

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|162275184|gb|FC451771.1|FC451771

EST:     GGTCTATCGGCAGGCATGGCCATTGGTATCGTCGGAGATGCTGGTGTTAG                         GGCCAATGCGCAACAGCCCAAGCTGTTTGTAGGAATGATCCTGATTCTGAT
genomic: GGTCTATCGGCAGGCATGGCCATTGGTATCGTCGGAGATGCTGGTGTTAGgtacttgaca ... ttttgtgcagGGCCAATGCGCAACAGCCCAAGCTGTTTGTAGGAATGATCCTGATTCTGAT

EST: gi|162207190|gb|FC382512.1|FC382512

EST:     GGTCTATCGGCAGGCATGGCCATTGGTATCGTCGGAGATGCTGGTGTTAG                         GGCCAATGCGCAACAGCCCAAGCTGTTTGTAGGAATGATCCTGATTCTGAT
genomic: GGTCTATCGGCAGGCATGGCCATTGGTATCGTCGGAGATGCTGGTGTTAGgtacttgaca ... ttttgtgcagGGCCAATGCGCAACAGCCCAAGCTGTTTGTAGGAATGATCCTGATTCTGAT

EST: gi|162212908|gb|FC388916.1|FC388916

EST:     GGTCTATCGGCAGGCATGGCCATTGGTATCGTCGGAGATGCTGGTGTTAG                         GGCCAATGCGCAACAGCCCAAGCTGTTTGTAGGAATGATCCTGATTCTGAT
genomic: GGTCTATCGGCAGGCATGGCCATTGGTATCGTCGGAGATGCTGGTGTTAGgtacttgaca ... ttttgtgcagGGCCAATGCGCAACAGCCCAAGCTGTTTGTAGGAATGATCCTGATTCTGAT

EST: gi|67709770|gb|BJ965586.1|BJ965586

EST:     GGTCTATCGGCAGGCATGGCCATTGGTATCGTCGGAGATGCTGGTGTTAG                         GGCCAATGCGCAACAGCCCAAGCTGTTTGTAGGAATGATCCTGATTCTGAT
genomic: GGTCTATCGGCAGGCATGGCCATTGGTATCGTCGGAGATGCTGGTGTTAGgtacttgaca ... ttttgtgcagGGCCAATGCGCAACAGCCCAAGCTGTTTGTAGGAATGATCCTGATTCTGAT

EST: gi|67723846|gb|BJ974105.1|BJ974105

EST:     GGTCTATCGGCAGGCATGGCCATTGGTATCGTCGGAGATGCTGGTGTTAG                         GGCCAATGCGCAACAGCCCAAGCTGTTTGTAGGAATGATCCTGATTCTGAT
genomic: GGTCTATCGGCAGGCATGGCCATTGGTATCGTCGGAGATGCTGGTGTTAGgtacttgaca ... ttttgtgcagGGCCAATGCGCAACAGCCCAAGCTGTTTGTAGGAATGATCCTGATTCTGAT

EST: gi|67721529|gb|BJ971788.1|BJ971788

EST:     GGTCTATCGGCAGGCATGGCCATTGGTATCGTCGGAGATGCCGGTGTTAG                         GGCCAATGCGCAACAGCCCAAGCTGTTTGTAGGAATGATCCTGATTCTGAT
genomic: GGTCTATCGGCAGGCATGGCCATTGGTATCGTCGGAGATGCTGGTGTTAGgtacttgaca ... ttttgtgcagGGCCAATGCGCAACAGCCCAAGCTGTTTGTAGGAATGATCCTGATTCTGAT

EST: gi|162275185|gb|FC451772.1|FC451772

EST:     GGTCTATCGGCAGGCATGGCCATTGGTATCGTCGGAGATGCTGGTGTTAG                         GGCCAATGCGCAACAGCCCAAGCTGTTTGTAGGAATGATCCTGATTCTGAT
genomic: GGTCTATCGGCAGGCATGGCCATTGGTATCGTCGGAGATGCTGGTGTTAGgtacttgaca ... ttttgtgcagGGCCAATGCGCAACAGCCCAAGCTGTTTGTAGGAATGATCCTGATTCTGAT

EST: gi|162207189|gb|FC382511.1|FC382511

EST:     GGTCTATCGGCAGGCATGGCCATTGGTATCGTTGGAGATGCTGGTGTTAG                         GGCCAATGCGCAACAGCCCAAGCTGTTTGTAGGAATGATCCTGATTTTGAT
genomic: GGTCTATCGGCAGGCATGGCCATTGGTATCGTCGGAGATGCTGGTGTTAGgtacttgaca ... ttttgtgcagGGCCAATGCGCAACAGCCCAAGCTGTTTGTAGGAATGATCCTGATTCTGAT

EST: gi|162262065|gb|FC437886.1|FC437886

EST:     GGTCTATCGGCAGGCATGGCCATTGGTATCGTCGGAGATGCTGGTGTTAG                         GGCCAATGCGCAACAGCCCAAGCTGTTTGTAGGAATGATCCTGATTCTGAT
genomic: GGTCTATCGGCAGGCATGGCCATTGGTATCGTCGGAGATGCTGGTGTTAGgtacttgaca ... ttttgtgcagGGCCAATGCGCAACAGCCCAAGCTGTTTGTAGGAATGATCCTGATTCTGAT

EST: gi|162262064|gb|FC437885.1|FC437885

EST:     GGTCTATCGGCAGGCATGGCCATTGGTATCGTCGGAGATGCTGGTGTTAG                         GGCCAATGCGCAACAGCCCAAGCTGTTTGTAGGAATGATCCTGATTCTGAT
genomic: GGTCTATCGGCAGGCATGGCCATTGGTATCGTCGGAGATGCTGGTGTTAGgtacttgaca ... ttttgtgcagGGCCAATGCGCAACAGCCCAAGCTGTTTGTAGGAATGATCCTGATTCTGAT

EST: gi|162212907|gb|FC388915.1|FC388915

EST:     GGTCTATCGGCAGGCATGGCCATTGGTATCGTCGGAGATGCTGGTGTTAG                         GGCCAATGCGCAACAGCCCAAGCTGTTTGTAGGAATGATCCTGATTCTGAT
genomic: GGTCTATCGGCAGGCATGGCCATTGGTATCGTCGGAGATGCTGGTGTTAGgtacttgaca ... ttttgtgcagGGCCAATGCGCAACAGCCCAAGCTGTTTGTAGGAATGATCCTGATTCTGAT

EST: gi|6167058|gb|AW145377.1|AW145377

EST:     GGTCTATCGGCAGGCATGGCCATTGGTATCGTCGGAGATGCTGGTGTTAG                         GGCCAATGCGCAACAGCCCAAGCTGTTTGTAGGAATGATCCTGATTCTGAT
genomic: GGTCTATCGGCAGGCATGGCCATTGGTATCGTCGGAGATGCTGGTGTTAGgtacttgaca ... ttttgtgcagGGCCAATGCGCAACAGCCCAAGCTGTTTGTAGGAATGATCCTGATTCTGAT

EST: gi|19783928|gb|BQ040091.1|BQ040091

EST:     GGTCTATCGGCAGGCATGGACATTGGTATCGTCGGAGATGCTGGAGTTAG                         GGCCAATGCGCAACAGCCCAAGCTGTTTGTAGGAATGATCCTGATTCTGAT
genomic: GGTCTATCGGCAGGCATGGCCATTGGTATCGTCGGAGATGCTGGTGTTAGgtacttgaca ... ttttgtgcagGGCCAATGCGCAACAGCCCAAGCTGTTTGTAGGAATGATCCTGATTCTGAT

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: 35 (upstream exon), 31 (downstream exon)
Score: 12

TGTTCGACGGCTACGCGCACCTTTCATCTGGATTGTCGTGTGGGTTGGCTGGTCTATCGGCAGGCATGGCCATTGGTATCGTCGGAGATGCTGGTGTTAGgtacttgaca ... ttttgtgcagGGCCAATGCGCAACAGCCCAAGCTGTTTGTAGGAATGATCCTGATTCTGATTTTCGCCGAGGCGCTGGCTTTATACGGACTTATCGTGGGTATCATTCTG

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atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tgatgccatttgttgatcatgtccttgttaacttggaggatggggttttgtgcagGGCCAATGCGCAACAGCCCAAGCTGTTTGTAGGAATGATCCTGATTCTGATTTTCGCCGAGGCGCTGGCTTTATACGGACTTATCGTGGGTATCATTCTG