ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtaagattgatgagttgtagacatatttcaagctctgactgattcatacttacgaccaaacatagttctgaaagtttcaaattaatgtgtgctcgtttggtactgagatggaggatttgagatcagccaaagtaagtcacgatgctgggttgtgattgtgtcactgaattcgcagATGAGAAGATAGCCCTTTTGGGTGCCATCCAGTCTTTGTTTGAGGGCTCCATGTACACATTTGTGTTCCTCTGGACACCAGCCTTGAGCCCCAACGATCA

Basic information

species	Physcomitrella patens
transcript	PP1S8_271V6.1
intron #	4
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: PP1S8_271V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: LOC_Os03g02380.2 (Oryza sativa), 3'ss of exon 4

gtaagattgatgagttgtagacatatttcaagctctgactgattcatacttacgaccaaacatagttctgaaagtttcaaattaatgtgtgctcgtttggtactgagatggaggatttgagatcagccaaagtaagtcacgatgctgggttgtgattgtgtcactgaattcgc-agATGAGAAGATAGCCCTTTTGGGTGCCATCCAGTCTTTGTTTGAGGGCTCCATGTACACATTTGTGTTCCTCTGGACACCAGCCTTGAGCCCCAACGATCA
                                                                            |    ||||    | ||  || | |     ||  ||  |   || ||    ||||||   | || || | |  || |||     ||  |||| ||   |||||| || || ||  |  |||| ||||| ||||| |||||||||||||| ||||| || || || ||||||||||| || || |||||||| || ||  |
---------------------------------------------------------------------------gtatgcttaactcat-cttattggatt----gacagataaacagatatgtatcaaagt---tgacaat-cggcattctgacatcatccttgaaatctttagATGAAAAAATTGCATTACTGGGAGCCATACAGTCATTGTTTGAGGGCTCAATGTATACTTTCGTCTTCCTCTGGACTCCGGCGTTGAGCCCAAATGAAGA

upper sequence: PP1S8_271V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G021514_T01 (Zea mays), 3'ss of exon 3

gtaagattgatgagttgtagacatatttcaagctctgactgattcatacttacgaccaaacatagttctgaaagtttcaaattaatgtgtgctcgtttggtac--tgagatggaggatttgagatcagccaaagtaagtcacgatgctgggttgtgattgtgtc-actgaattcgcagATGAGAAGATAGCCCTTTTGGGTGCCATCCAGTCTTTGTTTGAGGGCTCCATGTACACATTTGTGTTCCTCTGGACACCAGCCTTGAGCCCCAACGATCA
                                                                                      || ||||       |    | |||  | | ||     |  |  || |  ||  |    |  ||  || | |   |||| | |  ||   ||||||| ||||| ||  |  |||| ||||| ||||| ||||||||||||||||||||||||||||| ||||| ||||| ||||| ||||| || || ||  |
--------------------------------------------------------------------------------------gtatgcttaacccatctcatcagactgcgcataaccaaatatgcatatgaaacctgtgt-ttgccttctaacgctgtccatttgatcttcagATGAAAAGATTGCATTACTGGGAGCCATACAGTCATTGTTTGAGGGCTCCATGTACACATTTGTCTTCCTATGGACTCCAGCATTGAGTCCAAATGAAGA

upper sequence: PP1S8_271V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G064563_T03 (Zea mays), 3'ss of exon 4

gtaagattgatgagttgtagacatatttcaagctctgactgattcatacttacgaccaaacatagttctgaaagtttcaaattaatgtgtgctcgtttggtac--tgagatggaggatttgagatcagccaaagtaagtcacgatgctgggttgtgattgtgtc-actgaattcgcagATGAGAAGATAGCCCTTTTGGGTGCCATCCAGTCTTTGTTTGAGGGCTCCATGTACACATTTGTGTTCCTCTGGACACCAGCCTTGAGCCCCAACGATCA
                                                                                      || ||||       |    | |||  | | ||     |  |  || |  ||  |    |  ||  |||| |   |||| | |  ||   ||||||| ||||| ||  |  |||| ||||| ||||| ||||||||||||||||||||||||||||| ||||| ||||| ||||| ||||| || || ||  |
--------------------------------------------------------------------------------------gtatgcttaacccatctcatcagactgcgcataaccaaatatgcatatgaaacctgtgt-ttgccttgtaacgctgtccatttgatcttcagATGAAAAGATTGCATTACTGGGAGCCATACAGTCATTGTTTGAGGGCTCCATGTACACATTTGTCTTCCTATGGACTCCAGCATTGAGTCCAAATGAAGA

upper sequence: PP1S8_271V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G077669_T01 (Zea mays), 3'ss of exon 4

gtaagattgatgagttgtagacatatttcaagctctgactgattcatacttacgaccaaacatagttctgaaagtttcaaattaatgtgtgctcgtttggtactgagatggaggatttgagatcagccaaagtaagtcacgatgctgggttgtgattgtgtc-actgaattcgcagATGAGAAGATAGCCCTTTTGGGTGCCATCCAGTCTTTGTTTGAGGGCTCCATGTACACATTTGTGTTCCTCTGGACACCAGCCTTGAGCCCCAACGATCA
                                                                                 |     |  || ||| |  |    |    ||| |    | ||      |  | |  |  |    ||  || | |    ||| |||| ||   ||||||| ||||| ||  |  |||| ||||| ||||| |||||||||||||| |||||||||||||| ||||| ||||| ||||| |||||||| || ||  |
--------------------------------------------------------------------------------gtatgctttagcccgtctcatcagaacgcagagaaccaaatatttatgcatatgaaacctgcatttgttttctaacatcgtccactggatcttcagATGAAAAGATTGCATTACTGGGAGCCATACAGTCATTGTTTGAGGGCTCGATGTACACATTTGTCTTCCTATGGACTCCAGCGTTGAGCCCAAATGAAGA

upper sequence: PP1S8_271V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: AT1G64650.2 (Arabidopsis thaliana), 3'ss of exon 2

gtaagattgatgagttgtagacatatttcaagctctgactgattcatacttacgaccaaacatagttctgaaagtttcaaattaatgtgtgctcgtttggtactgagatggaggatttgagatcagccaaagtaagtcacgatgctgggttgtgattgtgtcactgaattcgcagATGAGAAGATAGCCCTTTTGGGTGCCATCCAGTCTTTGTTTGAGGGCTCCATGTACACATTTGTGTTCCTCTGGACACCAGCCTTGAGCCCCAACGATCA
                                                                    ||||  | | |  |||   || | |  |    |||||  ||   |  ||||    ||||   | |    ||| |  |         |   | | | | |||   ||||||||||||| ||  |  | ||||| || |||||| ||||||| || ||||||||||| |||||||| |||||||| || || |||||||| |||||  |
-------------------------------------------------------------------gtgaatctcttaccttaccttg-gtttttgacatactgtaatat-gtctttgcttccagctttattcttccactaacc---------acctttttattaaat---cagATGAGAAGATCGCATTACTCGGTGCTATTCAGTCTCTGTTTGAAGGGTCCATGTACACCTTTGTGTTTCTCTGGACTCCTGCTTTGAGCCCAAACGAAGA

upper sequence: PP1S8_271V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: AT4G27720.1 (Arabidopsis thaliana), 3'ss of exon 4

gtaagattgatgagttgtagacatatttcaagctctgactgattcatacttacgaccaaacatagttctgaaagtttcaaattaatgtgtgctcgtttggtactgagatggaggatttgagatcagccaaagtaagtcacgatgctgggttgtgattgtgtcactgaattcgcagATGAGAAGATAGCCCTTTTGGGTGCCATCCAGTCTTTGTTTGAGGGCTCCATGTACACATTTGTGTTCCTCTGGACACCAGCCTTGAGCCCCAACGATCA
          ||||| | | |  |  ||   || |    |   |  ||||| |       | |   ||||     |  |   | |||  |    |||| ||       ||      ||||        | | |   | | | |       | |  |||| ||  | |     |||||||||||||||| || |||||||| ||||||||  | ||||| || || ||||| || ||||| ||||||||||| || ||  | || || |||||| |
---------gtgagtagaaaatcttgtt---gccccttttagattttacttcctgttttgctt--ctctg-----tctattgtgatggttctgtgttttgtttctcattgtcctcattga--------agaatgtatgatggtaacaaaattt--ttgtatcttttat----cagATGAGAAGATAGCACTATTGGGTGCTATCCAGTCGCTCTTTGAAGGATCTATGTATACTTTTGTATTCCTCTGGACTCCTGCTCTAAGTCCGAACGATGA

upper sequence: PP1S8_271V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: Vv16s0098g01290.t01 (Vitis vinifera), 3'ss of exon 4

gtaagattgatgagttgtagacatatttcaagctctgactgattcatacttacgaccaaacatagttctgaaagtttcaaattaatgtgtgctcgtttggtactgagatggaggatttgagatcagccaaagtaagtcacgatgctgggttgtgattgtgtcactgaattcgcagATGAGAAGATAGCCCTTTTGGGTGCCATCCAGTCTTTGTTTGAGGGCTCCATGTACACATTTGTGTTCCTCTGGACACCAGCCTTGAGCCCCAACGATCA
                                                            ||| |||    |   | | |||   | | |   | | || | |            ||| || |    |    |   ||  |  |||    | | || || |||     |||  ||||||||| || ||  |  ||||||| || ||||| |||||||| ||||| ||||| || ||||||||||||||||| || ||  | ||||| || ||  |
------------------------------------------------------------cattgtttgcta---tcccaatgggtttat--ccatctgtttcctcatct-----tttcagttttttcctcctt--tcttggagctttagtattat-gtttcatgtggttc--agATGAGAAAATTGCGTTGCTGGGTGCAATTCAGTCGTTGTTTGAAGGCTCAATGTATACTTTTGTGTTCCTCTGGACTCCTGCTCTAAGCCCAAATGAAGA

upper sequence: PP1S8_271V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: Vv02s0025g02420.t01 (Vitis vinifera), 3'ss of exon 4

gtaagattgatgagttgtagacatatttcaagctctgactgattcatacttacgaccaaacatagttctgaaagtttcaaattaatgtgtgctcgtttggtactgagatggaggatttgagatcagccaaagtaagtcacgatgctgggttgtgattgtgtcactgaattcgcagATGAGAAGATAGCCCTTTTGGGTGCCATCCAGTCTTTGTTTGAGGGCTCCATGTACACATTTGTGTTCCTCTGGACACCAGCCTTGAGCCCCAACGATCA
                                                                           |  |  ||  |   | ||  |||| |  |    |  | | || ||  |             ||    |  |    | |  || |||  |        |||||||||| |||||  |  ||||||| || |||||| | ||||| || || |||||||||||||||||||| ||||| || || ||||| || || ||  |
--------------------------------------------------------------------------atatattttctttctttcttctttgat-ttattttatatgcttggaagtttcttttttattttctttttattttaatattgttatgtttcatgtggatcagATGAGAAAATAGCATTGCTGGGTGCAATACAGTCTCTATTTGAAGGTTCAATGTACACATTTGTGTTCCTTTGGACTCCTGCTTTGAGTCCGAATGAAGA

upper sequence: PP1S8_271V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ21113 (Selaginella moellendorffii), 3'ss of exon 4

gtaagattgatgagttgtagacatatttcaagctctgactgattcatacttacgaccaaacatagttctgaaagtttcaaattaatgtgtgctcgtttggtactgagatggaggatttgagatcagccaaagtaagtcacgatgctgggttgtgattgtgtcactgaattc---gcagATGAGAAGATAGCCCTTTTGGGTGCCATCCAGTCTTTGTTTGAGGGCTCCATGTACACATTTGTGTTCCTCTGGACACCAGCCTTGAGCCCCAACGATCA
                                                                                                                          | |||      | |||   ||||   |         | ||  || ||||   | |||||| ||||| || ||  | || || ||||| ||| | || ||||||||||||||||| || || ||||||||||| || || ||||| || ||||||||
-------------------------------------------------------------------------------------------------------------------------gtaagctttt-catgtctttatgc-aagcgagagccttatctttggattctatgtagATGAAAAGATTGCTCTCCTAGGAGCAATCCAATCTCTCTTCGAGGGCTCCATGTACACTTTCGTCTTCCTCTGGACGCCTGCATTGAGTCCTAACGATCA

upper sequence: PP1S8_271V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ11977 (Selaginella moellendorffii), 3'ss of exon 4

gtaagattgatgagttgtagacatatttcaagctctgactgattcatacttacgaccaaacatagttctgaaagtttcaaattaatgtgtgctcgtttggtactgagatggaggatttgagatcagccaaagtaagtcacgatgctgggttgtgattgtgtcactgaattcgcagATGAGAAGATAGCCCTTTTGGGTGCCATCCAGTCTTTGTTTGAGGGCTCCATGTACACATTTGTGTTCCTCTGGACACCAGCCTTGAGCCCCAACGATCA
                                                                                                             | | | |||          || | |||  |      |   ||  |||| | |          | |||||| ||||| || ||  | || || ||||| ||| | || ||||||||||||||||| || || ||||||||||| || || ||||| || ||||||||
-------------------------------------------------------------------------------------------------------------gtaagcttttcatgtctttaatgcaagcgagagccttatctttggattctat----------gtagATGAAAAGATTGCTCTCCTAGGAGCAATCCAATCTCTCTTCGAGGGCTCCATGTACACTTTCGTCTTCCTCTGGACGCCTGCATTGAGTCCTAACGATCA

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|162192969|gb|FC371952.1|FC371952

EST:     CAAAAGCTTCACGCATCAATTTACGCAGGCAGCTTCAGCTATTGCTTCTG                         ATGAGAAGATAGCCCTTTTGGGTGCCATCCAGTCTTTGTTTGAGGGCTCCA
genomic: CAAAAGCTTCACGCATCAATTTACGCAGGCAGCTTCAGCTATTGCTTCTGgtaagattga ... gaattcgcagATGAGAAGATAGCCCTTTTGGGTGCCATCCAGTCTTTGTTTGAGGGCTCCA

EST: gi|162160906|gb|FC336969.1|FC336969

EST:     CAAAAGCTTCACGCATCAATTTACGCAGGCAGCTTCAGCTATTGCTTCTG                         ATGAGAAGATAGCCCTTTTGGGTGCCATCCAGTCTTTGTTTGAGGGCTCCA
genomic: CAAAAGCTTCACGCATCAATTTACGCAGGCAGCTTCAGCTATTGCTTCTGgtaagattga ... gaattcgcagATGAGAAGATAGCCCTTTTGGGTGCCATCCAGTCTTTGTTTGAGGGCTCCA

EST: gi|162272123|gb|FC447917.1|FC447917

EST:     CAAAAGCTTCACGCATCAATTTACGCAGGCAGCTTCAGCTATTGCTTCTG                         ATGAGAAGATAGCCCTTTTGGGTGCCATCCAGTCTTTGTTTGAGGGCTCCA
genomic: CAAAAGCTTCACGCATCAATTTACGCAGGCAGCTTCAGCTATTGCTTCTGgtaagattga ... gaattcgcagATGAGAAGATAGCCCTTTTGGGTGCCATCCAGTCTTTGTTTGAGGGCTCCA

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: 33 (upstream exon), 27 (downstream exon)
Score: 6

GCCATTATTATCTCTTTTTGGCCGGAGAACTATGGAGATCAGACGGAAGGCAAAAGCTTCACGCATCAATTTACGCAGGCAGCTTCAGCTATTGCTTCTGgtaagattga ... gaattcgcagATGAGAAGATAGCCCTTTTGGGTGCCATCCAGTCTTTGTTTGAGGGCTCCATGTACACATTTGTGTTCCTCTGGACACCAGCCTTGAGCCCCAACGATCA

<

<

<

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

gatcagccaaagtaagtcacgatgctgggttgtgattgtgtcactgaattcgcagATGAGAAGATAGCCCTTTTGGGTGCCATCCAGTCTTTGTTTGAGGGCTCCATGTACACATTTGTGTTCCTCTGGACACCAGCCTTGAGCCCCAACGATCA