ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtacttgaagaaatcataatgttcttttgtactagcattatcttagctgagcttaccctttttttattaattggcagCCTGATTCACTCGGACCACTGGACTTGGACATACCGTCTGTGAGATACGAAGCCGATGACATACTTATAGGGGACAGTCAAAATAGTTGGAACCGTCTAA

Basic information

species	Zea mays
transcript	GRMZM2G104255_T01
intron #	3
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G104255_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g13790.1 (Oryza sativa), 3'ss of exon 12

-------gtacttgaagaaatcataa-tgttcttttgtactagcattatcttagctgagcttaccctttttttattaattggcagCCTGATTCACTCGGACCACTGGACTTGGACATACCGTCTGTGAGATACGAAGCCGATGACATACTTATAGGGGACAGTCAAAATAGTTGGAACCGTCTAA
         |  ||    |  ||||  |||| | || |  | |  | ||  |     | || | |  | || | |    || |||||||||||||| |||||| ||||||||||||||||||| | || |||| | || |||||| ||||  |||||||||| || ||||||||||||||  | |
gtactatacaaatgtcctatccatacctgttttcttttcatggtgtaatgctcat--aactaaacaatcttctctc--ctgacagCCTGATTCACTTGGACCATTGGACTTGGACATACCGTCCGCGACATACCATGCTGATGACTTACTCCTAGGGGACAGCCAGAATAGTTGGAACCGCATGA

upper sequence: GRMZM2G104255_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g56234.2 (Oryza sativa), 3'ss of exon 12

gtacttga-agaaatcataatgtt--cttttgta----ctagcattatc--ttagctgagcttac------cctttttttattaattggcagCCTGATTCACTCGGACCACTGGACTTGGACATACCGTCTGTGAGATACGAAGCCGATGACATACTTATAGGGGACAGTCAAAATAGTTGGAACCGTCTAA
||||| || ||| ||| ||    |  || || ||    |||| || |||  | | |  || | |       |  | | || |   | |  || |||||||||| |||||||||||||| || ||||| || ||||||||| |||| || ||| ||||  |||| |||||||| ||||||||||| ||  | |
gtactagacagatatcctatccctgcctgttttagtttctagtataatctatcaacacagatcataacttactatgtcttctctttggatagGCTGATTCACTTGGACCACTGGACTTAGAGATACCATCCGTGAGATACCAAGCTGAGGACTTACTCTTAGGAGACAGTCAGAATAGTTGGAATCGCATGA

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|71307078|gb|DR789707.1|DR789707

EST:     ATGATGAAACTAATGAGTTGAAGGATCAATCTTTAGCTGACATATATTGG                         CCTGATTCACTCGGACCACTGGACTTGGACATACCGTCTGTGAGATACGAA
genomic: ATGATGAAACTAATGAGTTGAAGGATCAATCTTTAGCTGACATATATTGGgtacttgaag ... taattggcagCCTGATTCACTCGGACCACTGGACTTGGACATACCGTCTGTGAGATACGAA

EST: gi|29945793|gb|CB815822.1|CB815822

EST:     ATGATGAAACTAATGAGTTGAAGGATCAATCTTTAGCTGACATATATTGG                         CCTGATTCACTCGGACCACTGGACTTGGACATACCGTCTGTGAGATACGAA
genomic: ATGATGAAACTAATGAGTTGAAGGATCAATCTTTAGCTGACATATATTGGgtacttgaag ... taattggcagCCTGATTCACTCGGACCACTGGACTTGGACATACCGTCTGTGAGATACGAA

EST: gi|93282287|gb|EB674551.1|EB674551

EST:     ATGATGAAACTAATGAGTTGAAGGATCAATCTTTAGTTGACATATATTGG                         CCTGATTCACTCGGACCACTGGACTTGGACATACCGTCTGTGAGATAGGAA
genomic: ATGATGAAACTAATGAGTTGAAGGATCAATCTTTAGCTGACATATATTGGgtacttgaag ... taattggcagCCTGATTCACTCGGACCACTGGACTTGGACATACCGTCTGTGAGATACGAA

EST: gi|211129534|gb|FL432598.1|FL432598

EST:     ATGATGAAACTAATGAGTTGAAGGATCAATCTTTAGCTGACATATATTGG                         CCTGATTCACTCGGACCACTGGACTTGGACATACCGTCTGTGAGATACGAA
genomic: ATGATGAAACTAATGAGTTGAAGGATCAATCTTTAGCTGACATATATTGGgtacttgaag ... taattggcagCCTGATTCACTCGGACCACTGGACTTGGACATACCGTCTGTGAGATACGAA

EST: gi|76281047|gb|DV020615.1|DV020615

EST:     ATGATGAAACTAATGAGTTGAAGGATCAATCTTTAGCTGACATATATTGG                         CCTGATTCACTCGGACCACTGGACTTGGACATACCGTCTGTGAGATACGAA
genomic: ATGATGAAACTAATGAGTTGAAGGATCAATCTTTAGCTGACATATATTGGgtacttgaag ... taattggcagCCTGATTCACTCGGACCACTGGACTTGGACATACCGTCTGTGAGATACGAA

EST: gi|76281086|gb|DV020654.1|DV020654

EST:     ATGATGAAACTAATGAGTTGAAGGATCAATCTTTAGCTGACATATATTGG                         CCTGATTCACTCGGACCACTGGACTTGGACATACCGTCTGTGAGATACGAA
genomic: ATGATGAAACTAATGAGTTGAAGGATCAATCTTTAGCTGACATATATTGGgtacttgaag ... taattggcagCCTGATTCACTCGGACCACTGGACTTGGACATACCGTCTGTGAGATACGAA

EST: gi|32931137|gb|CF035949.1|CF035949

EST:     ATGATGAAACTAATGAGTTGAAGGATCAATCTTTAGCTGACATATATTGG                         CCTGATTCACTCGGACCACTGGACTTGGACATACCGTTTGTGAGATACGAA
genomic: ATGATGAAACTAATGAGTTGAAGGATCAATCTTTAGCTGACATATATTGGgtacttgaag ... taattggcagCCTGATTCACTCGGACCACTGGACTTGGACATACCGTCTGTGAGATACGAA

EST: gi|76281048|gb|DV020616.1|DV020616

EST:     ATGATGAAACTAATGAGTTGAAGGATCAATCTTTAGCTGACATATATTGG                         CCTGATTCACTCGGACCACTGGACTTGGACATACCGTCTGTGAGATACGAA
genomic: ATGATGAAACTAATGAGTTGAAGGATCAATCTTTAGCTGACATATATTGGgtacttgaag ... taattggcagCCTGATTCACTCGGACCACTGGACTTGGACATACCGTCTGTGAGATACGAA

EST: gi|71307077|gb|DR789706.1|DR789706

EST:     ATGATGAAACTAATGAGTTGAAGGATCAATCTTTAGCTGACATATATTGG                         CCTGATTCACTCGGACCACTGGACTTGGACATACCGTCTGTGAGATACGAA
genomic: ATGATGAAACTAATGAGTTGAAGGATCAATCTTTAGCTGACATATATTGGgtacttgaag ... taattggcagCCTGATTCACTCGGACCACTGGACTTGGACATACCGTCTGTGAGATACGAA

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: 48 (upstream exon), 49 (downstream exon)
Score: 93

TAATGATGATGCCAAAGACGAGGAGTTTTATGCCAAATCACCACCTCGAAATGATGAAACTAATGAGTTGAAGGATCAATCTTTAGCTGACATATATTGGgtacttgaag ... taattggcagCCTGATTCACTCGGACCACTGGACTTGGACATACCGTCTGTGAGATACGAAGCCGATGACATACTTATAGGGGACAGTCAAAATAGTTGGAACCGTCTAA

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 66

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 76

Block sizes: 44 (upstream exon), 44 (downstream exon)
Score: 35

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tcttttgtactagcattatcttagctgagcttaccctttttttattaattggcagCCTGATTCACTCGGACCACTGGACTTGGACATACCGTCTGTGAGATACGAAGCCGATGACATACTTATAGGGGACAGTCAAAATAGTTGGAACCGTCTAA