ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtaattttcactcctttgttttatctgcagtttaatttgttctacaacaaaggtaaatctgttgtaaagtgttgtgtcgctcctttgctggtaatttctgcccccctccccttcaaacagACTAGCAGCGATTTCGATGCGAAGCCAATGGTCATGCTGTTGGGTCAATACTCCACGGGGAAAACAACATTCATAAAGCATTTACTAAAAACAAGTTATC

Basic information

species	Zea mays
transcript	GRMZM2G065012_T02
intron #	8
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G065012_T03 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os04g57350.1 (Oryza sativa), 3'ss of exon 8

gtaattttcactcctttgttttatctgcagtttaa-tttgttctacaacaaaggtaaatctgttgtaaagtgttgtgt-cgctcctttgctggtaatttctgcccc---cctccccttcaaacagACTAGCAGCGATTTCGATGCGAAGCCAATGGTCATGCTGTTGGGTCAATACTCCACGGGGAAAACAACATTCATAAAGCATTTACTAAAAACAAGTTATC
                         || ||   || ||||      ||||| |       |  | | |  ||   ||   |      |  |||   ||||| |  |     |  || |     |||||||||| ||||||||||||||||||||||||||| || ||||||| || ||||| || ||||| |||||||||||||||||||| || |||| |||||
-------------------------tgaagaaaaagtttggaactaaacaaggcctctattcctctcagttggcatgcatgacttcctaatggagctttctacgtcatgtttttccattttgtagACTAGCAGTGATTTCGATGCGAAGCCAATGGTCATGTTGCTGGGTCAGTATTCCACAGGAAAAACCACATTCATAAAGCATTTACTGAAGACAAATTATC

upper sequence: GRMZM2G065012_T03 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA17G01310.1 (Glycine max), 3'ss of exon 8

----gtaattttcactcctttgttttatctgcagtttaatttgttctaca-acaaaggtaaatctgttgtaaagtgttgtgtcgctcctttgctggtaatttctgcccccctccccttcaaacagACTAGCAGCGATTTCGATGCGAAGCCAATGGTCATGCTGTTGGGTCAATACTCCACGGGGAAAACAACATTCATAAAGCATTTACTAAAAACAAGTTATC
    || |  |  || ||     || ||   ||   | |  | || | || ||||| || | | |      || |||  |     |   ||  |   ||| ||||        |  |     ||||| | ||| ||||| ||||| || ||||||||||||||  | |||||||| ||||| ||||||||||| || ||||| |||||||||| |     |||||
gttagtgacatatacacccaatattaattaaca---tgacatattattcatacaaatgtgattattcatacaaatgtgattatattaagtt--taagaatgtctgtggtgtgtcttt-----cagACCAACAGTGATTTTGATGCTAAACCAATGGTCATGCTCCTTGGTCAATATTCCACTGGGAAAACAACCTTTATAAAACATTTACTAAGATGTGATTATC

upper sequence: GRMZM2G065012_T03 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA18G10150.1 (Glycine max), 3'ss of exon 7

----------------------------------------------gtaattttcactcctttgttttatctgcagtttaatttgttctacaacaaaggtaaatctgttgtaaagtgt-tgtgtcgctcctttgctggtaatttctgcccccctccccttcaaacagACTAGCAGCGATTTCGATGCGAAGCCAATGGTCATGCTGTTGGGTCAATACTCCACGGGGAAAACAACATTCATAAAGCATTTACTAAAAACAAGTTATC
                                                  |  |   |  ||||||| || ||    || | |  |   |  || |   || ||     | ||  | |   | | | |  |||  ||   |||  |   ||  || | ||    ||||| |  || || || ||||| || || |||||  |||| |||||||||||||| || |||||||||||||| || |||||| | || ||||  |||||||
gttagtaagtgattttatttatttggtttaattgagaaaacaagacaagctactttattttttgtttcatttgttaattcaataatctaatgaccattatatataaagagaaagatatacatttaggttatttattg---attgttattcctttctcattt---cagACAAATAGTGACTTTGATGCCAAACCTATGGTTTTGCTTTTGGGTCAATACTCAACTGGGAAAACAACATTTATTAAGCATATGCTTAAAAGCAGTTATC

upper sequence: GRMZM2G065012_T03 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA07G39450.1 (Glycine max), 3'ss of exon 8

----gtaattttcactcctttgttttatctgcagttt--aatttgt-tctacaacaaaggtaaatctgttgtaaagtgttgtgtcgctcctttgctggtaatt----tctgccc---------ccctccccttcaaacagACTAGCAGCGATTTCGATGCGAAGCCAATGGTCATGCTGTTGGGTCAATACTCCACGGGGAAAACAACATTCATAAAGCATTTACTAAAAACAAGTTATC
    || |  |  || ||     | ||  |  | | |  ||||| | |  || ||| | || ||| |    |||| ||   | |   || |      || |||    |  |                     ||   ||||| | ||| ||||| ||||| || ||||||||||||||  | |||||||| ||||| ||||||||||| |||||||| |||||||||| |     |||||
gttagtgacatatacacccaatatataaataaaatatggaatttttgtgaactacacatgttaatatcaattaaaatgacattttattcatgcaaatgtgattatattaagtttaagaatggttttggtttgtctttcagACCAACAGTGATTTTGATGCTAAACCAATGGTCATGCTCCTTGGTCAATATTCCACAGGGAAAACAACCTTCATAAAACATTTACTAAGATGTGATTATC

upper sequence: GRMZM2G065012_T03 (Zea mays), 3'ss of exon 8
lower sequence: AT4G05520.1 (Arabidopsis thaliana), 3'ss of exon 8

----gtaattttc--actccttt-gttttatctgcag--tttaatttgttctacaacaaaggtaaatctgttgtaaagtgttgt--gtcgctcctttgctggtaatt-tctgcccccctccccttcaaa-----cagACTAGCAGCGATTTCGATGCGAAGCCAATGGTCATGCTGTTGGGTCAATACTCCACGGGGAAAACAACATTCATAAAGCATTTACTAAAAACAAGTTATC
    ||||| | |  |||  ||  |    |  ||     |||  ||| |||         ||| ||    |    || |  | |   |  | || | |    | ||| || |          ||| |       |||||||| |||||||| ||||| || |||||||| ||||| ||||||||||| ||||| || ||||||||||| ||||| || || ||   |      || |
gtgagtaatatccttactgtttcagaaacacttgtgagtttttgtttattccgttttttcggtgaagagctaaagaactcatatctatatcaccatggaaaatgattctcagtttattgatactttatgatttgcagACTAGTAGCGATTTTGATGCCAAACCAATGGTAATGCTTTTGGGTCAATATTCCACCGGAAAAACAACATTTATAAAACACTTGCTCGGATGTGACTACC

upper sequence: GRMZM2G065012_T03 (Zea mays), 3'ss of exon 8
lower sequence: AT3G20290.2 (Arabidopsis thaliana), 3'ss of exon 8

gtaattttcac-tcctttgttttatctgcagtttaatttgttctacaacaaaggtaaatctgttgtaaagtgttgtgtcgctcctttgctggtaatttctgcccccctccccttcaaacagACTAGCAGCGATTTCGATGCGAAGCCAATGGTCATGCTGTTGGGTCAATACTCCACGGGGAAAACAACATTCATAAAGCATTTACTAAAAACAAGTTATC
|| | ||   | |   || ||    || |  |    ||  ||      ||||    | |   || |||| | |  | |  |   |   || || | || |       |   |||     |||||| ||| ||||||||||| || || ||||| |||||  |||||||||||||||| || |||||||||||||| |||||||| || ||| | | |||||
gtgagttgggcattgcttattggtgctcctatggcgttatttaagttccaaatactattgaattctaaactat-atttgaccattgaactagttacttgt----tttttttctt-----agACTAACAGTGATTTCGATGCAAAACCTATGGTAATGCTTCTGGGTCAATACTCCACAGGAAAAACAACATTCATTAAGCATTTGCTTAAATCTACTTATC

upper sequence: GRMZM2G065012_T03 (Zea mays), 3'ss of exon 8
lower sequence: Vv00s0516g00020.t01 (Vitis vinifera), 3'ss of exon 9

-------------------------------------------------------------gtaattttcact---cctttgttttatctgcagtttaatttgttctacaacaaaggtaaatctgttgtaaagtgttgtgtc--gctcc----------tttgc-----tggtaatttctgcccccctccccttcaaacagACTAGCAGCGATTTCGATGCGAAGCCAATGGTCATGCTGTTGGGTCAATACTCCACGGGGAAAACAACATTCATAAAGCATTTACTAAAAACAAGTTATC
                                                              |   | || ||   ||| |||   |  ||   |  ||  |||  ||  |   | |      | | ||| | |  ||  ||  |||||          ||||      ||| ||| | |       |  | ||    |||||    || || || ||||| || || ||||| ||||| |||||||| || || || |||||||| ||||||||||| ||||||||   |   | ||  |
gtaagtggactgagtattttagtttgtttatgatgagatgcctaaatttgttaatgatgagatgtctctcccttttcctatgtaacacatgttctaaaaaatgtgatattatgtatgctctgttctcgtagatttctgactctagctccagaagttctatttgagagtatggaaatattttttattttttctttt--gcagACACATAGTGACTTTGATGCCAAACCCATGGTTATGCTTTTGGGTCAGTATTCAACTGGGAAAACTACATTCATAAAACATTTACTCGGATGTAATTTCC

upper sequence: GRMZM2G065012_T03 (Zea mays), 3'ss of exon 8
lower sequence: Vv19s0090g01130.t01 (Vitis vinifera), 3'ss of exon 8

------------------------------------------------------gtaattttcactcctttgttttatctgcagtttaatttgt-tctacaacaaaggtaaatctgttgtaaagtgttgtgtcgctcctttgctggtaatttctgcccccctccccttcaaacagACTAGCAGCGATTTCGATGCGAAGCCAATGGTCATGCTGTTGGGTCAATACTCCACGGGGAAAACAACATTCATAAAGCATTTACTAAAAACAAGTTATC
                                                       |||| || | ||   ||  |  |     |||| ||||   ||||   | |   |  |     || | | || | | |       ||     |   |  ||      |     |    ||||| |  |||||||| ||||| || || ||||| ||||| |||||||||||||| || || ||||| || ||||| || ||||| || || |  |||||||
gtaagcgagaaatacacccagcttttaattgctttcatcctcagaaatagcaaaataatcttgattctaatgaatgttt----gtttgatttacatctattgctatattttaaaccatggacaatgatatataatgagcttatcacttgctgttgatgtgttatttgtt--gcagACAAATAGCGATTTTGATGCCAAACCTATGGTTATGCTTTTGGGTCAATACTCAACTGGAAAAACTACTTTCATTAAACATTTGCTGAAGAGTAGTTATC

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|71769027|gb|DR966964.1|DR966964

EST:     GGCCCTTGGAAAAAACCTATCAGTTCCATGACTTCGTGTCTCCCTTGCTG                         ACTAGCAGCGATTTCGATGCGAAGCCAATGGTCATGCTGTTGGGTCAATAC
genomic: GGCCCTTGGAAAAAACCTATCAGTTCCATGACTTCGTGTCTCCCTTGCTGgtaattttca ... cttcaaacagACTAGCAGCGATTTCGATGCGAAGCCAATGGTCATGCTGTTGGGTCAATAC

EST: gi|50323441|gb|CO518567.1|CO518567

EST:     CTATCAGTTCCATGACTTCGTGTCTCCCTTGCTG                         ACTAGCAGCGATTTCGATGCGAAGCCAATGGTCATGCTGTTGGGTCAATAC
genomic: CTATCAGTTCCATGACTTCGTGTCTCCCTTGCTGgtaattttca ... cttcaaacagACTAGCAGCGATTTCGATGCGAAGCCAATGGTCATGCTGTTGGGTCAATAC

EST: gi|78124010|gb|DV542394.1|DV542394

EST:     GGCCCTTGGAAAAAACCTATCAGTTCCGTGACTTCGTGTCTCCCTTGCTG                         ACTAGCAGCGATTTCGATGCAAAGCCAGGGGTCGTGCTGTGGGGTCAATAC
genomic: GGCCCTTGGAAAAAACCTATCAGTTCCATGACTTCGTGTCTCCCTTGCTGgtaattttca ... cttcaaacagACTAGCAGCGATTTCGATGCGAAGCCAATGGTCATGCTGTTGGGTCAATAC

EST: gi|71333237|gb|DR803673.1|DR803673

EST:     GGCCCTTGGAAAAAACCTATCAGTTCCATGACTTCGTGTCTCCCTTGCTG                         ACTAGCAGCGATTTCGATGCGAAGCCAATGGTCATGCTGTTGGGTCAATAC
genomic: GGCCCTTGGAAAAAACCTATCAGTTCCATGACTTCGTGTCTCCCTTGCTGgtaattttca ... cttcaaacagACTAGCAGCGATTTCGATGCGAAGCCAATGGTCATGCTGTTGGGTCAATAC

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: 48 (upstream exon), 46 (downstream exon)
Score: 77

AGTCACTTCAATCGTCGATGGGCTAAAGAAATCGTACATTGAGAAGTTGAGGCCCTTGGAAAAAACCTATCAGTTCCATGACTTCGTGTCTCCCTTGCTGgtaattttca ... cttcaaacagACTAGCAGCGATTTCGATGCGAAGCCAATGGTCATGCTGTTGGGTCAATACTCCACGGGGAAAACAACATTCATAAAGCATTTACTAAAAACAAGTTATC

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atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

aaagtgttgtgtcgctcctttgctggtaatttctgcccccctccccttcaaacagACTAGCAGCGATTTCGATGCGAAGCCAATGGTCATGCTGTTGGGTCAATACTCCACGGGGAAAACAACATTCATAAAGCATTTACTAAAAACAAGTTATC