ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtaagtatattagctagtaccaaccacatggtacctatcccatgtaccaaggcagtttatatatttgtcagactgttgtggttcatctgctcatggttatctagtttgttgttatgatatattatgataatgtgctccttgcggtctatattggtgcagCTAATGTATTCCATCGTGATCTAAAGCCCAAGAATATACTGGCTAACTCGGACTGCAAACTGAAAATATGTGACTTTGGACTTGCCCGTGCATCATTCAA

Basic information

species	Zea mays
transcript	GRMZM2G135904_T02
intron #	2
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G135904_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os06g49430.1 (Oryza sativa), 3'ss of exon 2

gtaagtatattagctagtaccaaccacatggtacctatcccatgtaccaaggcagtttatatatttgtcagactgttgtggttcatctgctcatggttatctagtttgttgttatgatatattatgataatgtgctccttgcggtctatattggtgcagCTAATGTATTCCATCGTGATCTAAAGCCCAAGAATATACTGGCTAACTCGGACTGCAAACTGAAAATATGTGACTTTGGACTTGCCCGTGCATCATTCAA
              ||     ||| || || ||     || ||   |||||           |  |    |||     |    ||  |  |  || | || || |   ||   |||  ||  ||   || | |           ||||||||||  ||||||||||||| ||||| |||||||||||||||||||||||||| ||||| ||||||||| ||||||||||||| || ||||||||||| |||||||||||
-------------gtaagcttaactac-tgataatc-cccaattccccaaga----------acctacttgaccaccattaaacacatagttctgttgattta-tcaattaacatggaattctagcttattctctgataaatcatctatattggcacagCTAATGTATTTCATCGCGATCTAAAGCCCAAGAATATACTGGCAAACTCAGACTGCAAATTGAAAATATGTGATTTCGGACTTGCCCGAGCATCATTCAA

upper sequence: GRMZM2G135904_T01 (Zea mays), 3'ss of exon 2
lower sequence: EDP02733 (Chlamydomonas reinhardtii), 3'ss of exon 4

gtaagtatattagctagtaccaaccacatggtacctatcccatgtaccaaggcagtttatatatttgtcagactgttgtggttcatctgctcatggttatctagtttgttgttatgatatattatgataatgtgctccttgcggtctatattggtgcagCTAATGTATTCCATCGTGATCTAAAGCCCAAGAATATACTGGCTAACTCGGACTGCAAACTGAAAATATGTGACTTTGGACTTGCCCGTGCATCATTCAA
                                                         |  |   | ||  | | ||  |||    |   |    | | | |  ||   |  |  |      |  |        |||||  |    ||       |||||| || || ||||| || || || ||||||||||| || ||||| ||||| ||||||||||| || |||||||                            
---------------------------------------------------------tgcagggtggtggggcggtgctggcg-gtgcaccggcgctgaccctgtccctcctcctccccgctcgt-----cccgctccgggtc-cctccccccctgcagccaagGTGTTCCACCGCGACCTCAAGCCCAAGAACATCCTGGCCAACTCCGACTGCAAACTCAAGATATGTG----------------------------

upper sequence: GRMZM2G135904_T01 (Zea mays), 3'ss of exon 2
lower sequence: PP1S87_157V6.2 (Physcomitrella patens), 3'ss of exon 2

gtaagtatattagctagtaccaaccacatggtacctatcccatgtaccaaggcagtttatatatttgtcagactgttgtggttcatctgctcatggttatctagtttgttgttatgatatattatgataatgtgctccttgcggtctatattggtgcagCTAATGTATTCCATCGTGATCTAAAGCCCAAGAATATACTGGCTAACTCGGACTGCAAACTGAAAATATGTGACTTTGGACTTGCCCGTGCATCATTCAA
                                                 |    ||   |||||||     |   | |||| | ||   || |||  | |   || | | |||  ||| |       | | ||||| ||    |    |  || |  |||||||||||| ||||| ||||| ||||| |||||| || |||| ||| | || ||||| |||||||| ||||| ||||||||||| || |   | |||| 
-----------------------------------------------tgaaaatgtaactatatttcaagaagaatagtggattatgatctaatgaatgt---gtgtctcgtttggatgt-------tgacgtgcttctatttgg--gtgatgctttagCTAATGTATTTCATCGCGATCTCAAGCCAAAGAATGTATTGGCAAACGCTGATTGCAAGCTGAAAATTTGTGATTTTGGACTTGCTCGGGTGGCTTTCAG

upper sequence: GRMZM2G135904_T01 (Zea mays), 3'ss of exon 2
lower sequence: PP1S80_71V6.2 (Physcomitrella patens), 3'ss of exon 2

gtaagtatattagctagtaccaaccacatggtacctatcccatgtaccaaggcagtttatatatttgtcagactgttgtggttcatctgctcatggttatctagtttgttgttatgatatattatgataatgtgctccttgcggtctatattggtgcagCTAATGTATTCCATCGTGATCTAAAGCCCAAGAATATACTGGCTAACTCGGACTGCAAACTGAAAATATGTGACTTTGGACTTGCCCGTGCATCATTCAA
                                               ||   |  |   | ||      |||||| || | |        |  ||| | ||| || |||| || ||       ||| | | ||  || |    || |    | || |||||||||| || ||||| || || ||||| |||||  |  |||| ||| | ||||| ||||||||||| ||||||||||||||||| || |   | || | 
----------------------------------------------tcacaactctcactgtac--aaaagactgatgggatgtggtcctttttggatttct-gtctgtttttgtgg------atgttgacgtcttcat----gtttgggattgttcagCTAATGTGTTTCATCGCGACCTGAAGCCAAAGAACGTGTTGGCAAACGCTGACTGTAAACTGAAAATTTGTGACTTTGGACTTGCTCGAGTGGCCTTTAG

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|67016391|gb|CO445140.1|CO445140

EST:     CCAGTTTTTCCTGTACCAACTTCTTCGAGCTCTCAAGTACATACATGCCG                         CTAATGTATTCCATCGCGATCTAAAGCCCAAGAATATACTGGCTAACTCGG
genomic: CCAGTTTTTCCTGTACCAACTTCTTCGAGCTCTCAAGTACATACATGCCGgtaagtatat ... attggtgcagCTAATGTATTCCATCGTGATCTAAAGCCCAAGAATATACTGGCTAACTCGG

EST: gi|22545672|gb|BU098031.1|BU098031

EST:     CCAGTTTTTCCTGTACCAACTTCTTCGAGCTCTCAAGTACATACATGCCG                         CTAATGTATTCCATCGTGATCTAAAGCCCAAGAATATACTGGCTAACTCGG
genomic: CCAGTTTTTCCTGTACCAACTTCTTCGAGCTCTCAAGTACATACATGCCGgtaagtatat ... attggtgcagCTAATGTATTCCATCGTGATCTAAAGCCCAAGAATATACTGGCTAACTCGG

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: 180

GATCTCCATCAAGTGATCAGGGCGAATGATGACCTCACCCCTGAACATCACCAGTTTTTCCTGTACCAACTTCTTCGAGCTCTCAAGTACATACATGCCGgtaagtatat ... attggtgcagCTAATGTATTCCATCGTGATCTAAAGCCCAAGAATATACTGGCTAACTCGGACTGCAAACTGAAAATATGTGACTTTGGACTTGCCCGTGCATCATTCAA

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 136

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 120

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 103

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tttgttgttatgatatattatgataatgtgctccttgcggtctatattggtgcagCTAATGTATTCCATCGTGATCTAAAGCCCAAGAATATACTGGCTAACTCGGACTGCAAACTGAAAATATGTGACTTTGGACTTGCCCGTGCATCATTCAA