ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

...gtttcctttgctgaaaatgcagctaataccaaacttgctgtttcctattgagatagatattctgttacttatcctttgtctcctcgtgtttttgttccagCATCATCAGTAACAAATGGCTGACGGTGAGGACATTCAGCCCCTTGTTTGTGACAATGGAACTGGCATGGTCAAG

Basic information

species	Zea mays
transcript	GRMZM2G126190_T02
intron #	1
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G126190_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os11g06390.6 (Oryza sativa), 3'ss of exon 1

---gtttcctttgctgaaaa---tgcagctaataccaaacttgctgtttcctattgagatagatattctgttacttatcctttgtc---tcctcgtgtttttgttccagCATCATCAGTAACAAATGGCTGACGGTGAGGACATTCAGCCCCTTGTTTGTGACAATGGAACTGGCATGGTCAAG
    |||  ||| ||| |     |||  ||| |  |    | |    |  | |||  |  |  | ||  |   | |  |  ||||    |  | | ||      | ||| | ||  || |  ||||||||||||| |||||||| ||||||||||| |||||||||||||||||||||||||||
agattttgatttcctggagggtttgcgtctagtttctg-ttggaaaatggccatttcgtgacgtgttgcggcgcatgcctgttgttctgtttttgcgtcagGAATTCAGAACCAGTAGGAGGAAATGGCTGACGGCGAGGACATCCAGCCCCTTGTGTGTGACAATGGAACTGGCATGGTCAAG

upper sequence: GRMZM2G126190_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os11g06390.5 (Oryza sativa), 3'ss of exon 1

gtttcctttgctgaaaatgcagctaataccaaacttgctgtttcctattgagatagatattctgttacttatcctttgtc---tcctcgtgtttttgttccagCATCATCAGTAACAAATGGCTGACGGTGAGGACATTCAGCCCCTTGTTTGTGACAATGGAACTGGCATGGTCAAG
 ||||||  |  |    |||  ||| |  |    | |    |  | |||  |  |  | ||  |   | |  |  ||||    |  | | ||      | ||| | ||  || |  ||||||||||||| |||||||| ||||||||||| |||||||||||||||||||||||||||
atttcct--ggagggtttgcgtctagtttctg-ttggaaaatggccatttcgtgacgtgttgcggcgcatgcctgttgttctgtttttgcgtcaggaattcagAACCAGTAGGAGGAAATGGCTGACGGCGAGGACATCCAGCCCCTTGTGTGTGACAATGGAACTGGCATGGTCAAG

upper sequence: GRMZM2G126190_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA06G15520.1 (Glycine max), 3'ss of exon 1

gtttcctttgctgaaaatgcagctaataccaaacttgctgtttcctattgagatagatattctg--ttacttatcctt-tgtctcctcgtgtttttgttccagCATCATCAGTAACAAATGGCTGACGGTGAGGACATTCAGCCCCTTGTTTGTGACAATGGAACTGGCATGGTCAAG
      ||||  | |||  |    | |    || | ||||  | || | ||  |   |||||    ||  |  | ||      |  | || |   |  |  ||     |  |||| |||||||||| | |||||| ||||| |||||||||||||||||||||||||| ||||| |||
--agagtttgaagtaaaccctcaaagtctgtaaatggctgggttctgtagat-tgtctattcaaacttggtggtactgacaatttattgtatgcgtactgtagT----TTGGTAAAAAATGGCTGATGCTGAGGATATTCAACCCCTTGTTTGTGACAATGGAACTGGAATGGTGAAG

upper sequence: GRMZM2G126190_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA04G39380.2 (Glycine max), 3'ss of exon 1

gtttcctttgctgaaaatgcagctaataccaaacttgctgtttcctattgagatagatattctgt-tacttatcctttgtctcctcgtgtttttgttcca-gCAT-CA-----TCAGTAACAAATGGCTGACGGTGAGGACATTCAGCCCCTTGTTTGTGACAATGGAACTGGCATGGTCAAG
        |   ||||||  |  ||||    ||  | ||||       || | |    |   ||| || | |  |||  |      |    ||||||| | |||| ||     |  |||| | |||||||| | |||||| ||||| |||||||| ||||||||||||||||| ||||| |||
--------tatagaaaataaacgtaatcttcaaagt-ctgtaagtggctgggttctgcagattgtctattcaaacttgttaatactggcaatttgttctatgcatacagTAGTTTGGTAAAAGATGGCTGATGCTGAGGATATTCAACCCCTTGTCTGTGACAATGGAACTGGAATGGTGAAG

upper sequence: GRMZM2G126190_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA04G39380.1 (Glycine max), 3'ss of exon 1

gtttcctttgctgaaaatgcagctaataccaaacttgctgtttcctattgagatagatattctgt-tacttatcctttgtctcctcgtgtttttgttcca-gCAT-CA-----TCAGTAACAAATGGCTGACGGTGAGGACATTCAGCCCCTTGTTTGTGACAATGGAACTGGCATGGTCAAG
            ||||||  |  ||||    ||  | ||||       || | |    |   ||| || | |  |||  |      |    ||||||| | |||| ||     |  |||| | |||||||| | |||||| ||||| |||||||| ||||||||||||||||| ||||| |||
-----------agaaaataaacgtaatcttcaaagt-ctgtaagtggctgggttctgcagattgtctattcaaacttgttaatactggcaatttgttctatgcatacagtagTTTGGTAAAAGATGGCTGATGCTGAGGATATTCAACCCCTTGTCTGTGACAATGGAACTGGAATGGTGAAG

upper sequence: GRMZM2G126190_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA08G15480.1 (Glycine max), 3'ss of exon 1

gtttcctttgctgaaaatgcagctaataccaaacttgctgtttcctattgagatagatattctg-ttacttatcctttgtctcctcgtgtttt-tgttccagCATCATCAGTAACAAATGGCTGACGGTGAGGACATTCAGCCCCTTGTTTGTGACAATGGAACTGGCATGGTCAAG
  ||| || |||| |||||   ||  |  |  ||  | |||  ||     | | |  | |  |  ||||| |  ||||   || | |     | || |         |  |||| | ||||| || |  ||||| ||||| ||||||||||| |||||||||||||| |||||||||
-cttcgttggctgtaaatgtc-ctggtttc--acgggttgt--ccatacaatacaattttgttacttactgacactttacttcatggcaccctatgctttctgtagGTTTGTAAAAGATGGCAGATGCCGAGGATATTCAACCCCTTGTTTGCGACAATGGAACTGGAATGGTCAAG

upper sequence: GRMZM2G126190_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA05G32220.2 (Glycine max), 3'ss of exon 1

gtttcctttgctgaaaatgcagctaataccaaacttgctgtttcctattgagatagatattctg-ttacttatcctttgtctcctcgtgtttt-tgttccagCATCATCAGTAACAAATGGCTGACGGTGAGGACATTCAGCCCCTTGTTTGTGACAATGGAACTGGCATGGTCAAG
      || |||| |||||       | |     ||| |  |        |  |  ||| | |  ||||| |  || | | || | |     | || |         |  |||| | ||||| || | |||||| ||||| |||||||||||||||||||||||||| |||||||||
------ttagctgtaaatgtcttggtttcacgggttgttcatataatacaatgtttatactttacttactgacactgtatttcatggcaccctatgctttttgcagGTTTGTAAAAGATGGCCGATGCTGAGGATATTCAACCCCTTGTTTGTGACAATGGAACTGGAATGGTCAAG

upper sequence: GRMZM2G126190_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA08G19420.1 (Glycine max), 3'ss of exon 1

gtttcctttgctgaaaatgcagctaataccaaacttgctgtttcctattgagatagatattctgttacttatcctttgtctcctcgtgtttttgttccagCATCATCAGTAACAAATGGCTGACGGTGAGGACATTCAGCCCCTTGTTTGTGACAATGGAACTGGCATGGTCAAG
     || |  | |   |  | ||  |             | |  | ||  | |   | || | || | | ||||      | |        |  ||    |       ||| |||||||||| | |||||||||||| || ||||||  ||| ||||||||||| |||||||||
----tctctagt-agtttcaaacttttgatcgttgcttcatcttttctttggttttgttttttatttcctttcctgaacaacttatctcccgttctctgctacagGTTTTAAAAAATGGCTGATGCTGAGGACATTCAACCTCTTGTTGTTGATAATGGAACTGGAATGGTCAAG

upper sequence: GRMZM2G126190_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA15G05570.1 (Glycine max), 3'ss of exon 1

gtttcctttgctgaaaatgcagctaataccaaacttgctgtttcctattgagatagatattctgttacttatcctttgtctcctcgtgtttttgttccagCATCATCAGTAACAAATGGCTGACGGTGAGGACATTCAGCCCCTTGTTTGTGACAATGGAACTGGCATGGTCAAG
    ||| |   |||  |  ||||  ||            | |  | ||  | |   |  | | ||| ||  |||      | || |     |  ||    |       ||| | |||||||| | |||||||||||| || ||||||  ||| ||||||||||| |||||||||
---gcctctctagaattttaagcttttaattgttgcatcatattttctttggtttcgttcttttttattt--cctaaacaacttctttcccgttctctgctacagGTTTTAAAAGATGGCTGATGCTGAGGACATTCAACCTCTTGTTGTTGATAATGGAACTGGAATGGTCAAG

upper sequence: GRMZM2G126190_T02 (Zea mays), 3'ss of exon 1
lower sequence: AT5G09810.1 (Arabidopsis thaliana), 3'ss of exon 1

gtttcctttgctgaaaatgcagctaatacc--aaactt-gctgtttcctattgagatagatattctgtta-cttatcctttgtctcctcgtgtttttgttccagCATCATCAGTAACAAATGGCTGACGGTGAGGACATTCAGCCCCTTGTTTGTGACAATGGAACTGGCATGGTCAAG
              ||| || ||||||     |||||  | |||   ||  |  | |   || |   | | |||||||  | ||   |||  ||  | || |    |  | ||| | ||||||| || |||||||| |||||||| ||||| ||||||||||||||||| ||||| |||
-----------aataaacgctgctaatcttcgaaactaagttgtgatctgattcg-tgtttacttcatgagcttatccaat-tcatttcggtttcattttactttttttttagTGAAAAATGGCCGATGGTGAGGATATTCAGCCACTTGTCTGTGACAATGGAACTGGAATGGTGAAG

upper sequence: GRMZM2G126190_T02 (Zea mays), 3'ss of exon 1
lower sequence: PP1S337_21V6.2 (Physcomitrella patens), 3'ss of exon 2

gtttcctttgctgaaaatgcagc-taataccaaacttgct-gtttcctattgagatagatatt--ctgttacttatcctttg--tctcctcgtgtttttgttccagCATCATCAGTAACAAATGGCTGACGGTGAGGACATTCAGCCCCTTGTTTGTGACAATGGAACTGGCATGGTCAAG
     |  |   ||    |     || |  |    ||||  |     | ||  ||   | |||  ||| | ||||    |    ||| ||    |  |||  |  |  ||   | ||| |||||||||||||||||||  | |||||| | || || |||||||||||||| |||||||||
-----cagtatggagggcgttctgtactgtcctgattgcgagacatgttttacgacgaaaatttactgctccttagaactaaaatcttctgaaatggttgggcagG--TCGGTATTAAGAAATGGCTGACGGTGAGGAAGTACAGCCCTTGGTGTGCGACAATGGAACTGGAATGGTCAAG

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|211160799|gb|FL123581.1|FL123581

EST:     GGAGGAATTAGTTCCGAATCTTTCTCCATTACGATTTTCGTGGCGTCGAG                         CATCATCAGTAACAAATGGCTGACGGTGAGGACATTCAGCCCCTTGTTTGT
genomic: GGAGGAATTAGTTCCGAATCTTTCTCCATTACGATTTTCGTGGCGTCGAGgttagtctga ... tttgttccagCATCATCAGTAACAAATGGCTGACGGTGAGGACATTCAGCCCCTTGTTTGT

EST: gi|33285526|gb|CF075321.1|CF075321

EST:     ATCTTTCTCCATTACGATTTTCGTGGCGTCGAG                         CATCATCAGTAACAAATGGCTGACGGTGAGGACATTCAGCCCCTTGTTTGT
genomic: ATCTTTCTCCATTACGATTTTCGTGGCGTCGAGgttagtctga ... tttgttccagCATCATCAGTAACAAATGGCTGACGGTGAGGACATTCAGCCCCTTGTTTGT

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: 40 (upstream exon), 49 (downstream exon)
Score: 30

GGCAGGTTCTCCTAGATCTCCGGGTAAGCGGTGAAAGAAGAGGAGGTGTTGGAGGAATTAGTTCCGAATCTTTCTCCATTACGATTTTCGTGGCGTCGAGgttagtctga ... tttgttccagCATCATCAGTAACAAATGGCTGACGGTGAGGACATTCAGCCCCTTGTTTGTGACAATGGAACTGGCATGGTCAAG

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 16

Block sizes: 46 (upstream exon), 46 (downstream exon)
Score: 14

Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 26

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tattgagatagatattctgttacttatcctttgtctcctcgtgtttttgttccagCATCATCAGTAACAAATGGCTGACGGTGAGGACATTCAGCCCCTTGTTTGTGACAATGGAACTGGCATGGTCAAG