ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gttgtctgaatgacttctatgttgtcacatatatcgatcactttatttcagttgtttctcattaatcttatgctctgggttgatctttagTTCTTTATCCTGAGGTTGGTGGAGGAACATTGGACTCCCATCACGCTTTTATTGTTGAATATGGGAAAGACAGGGATGTTGAACTAG

Basic information

species	Zea mays
transcript	GRMZM2G027311_T01
intron #	4
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G027311_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g31770.2 (Oryza sativa), 3'ss of exon 4

gttgtctgaatgacttctatg-ttgtcacatata---tcgatcactt---tatttcagttgtttctc----attaatcttatgctctgggttgatctttagTTCTTTATCCTGAGGTTGGTGGAGGAACATTGGACTCCCATCACGCTTTTATTGTTGAATATGGGAAAGACAGGGATGTTGAACTAG
||| ||| |  |||| ||||  |||| | ||| |      ||||||    | ||  |  | | | ||    ||| || ||||||| ||  || ||||| |||  | |||||||||||||||||||||||||| ||  | || || |||||| ||||||| |||||||||||||||||||||||||| |
gttatcttatcgactgctatccttgttaaatagaggcagaatcactagcattttcaaaatatatttcctatattgattttatgctgtg--ttaatcttcagTATTATATCCTGAGGTTGGTGGAGGAACATTAGATACACACCATGCTTTTGTTGTTGAGTATGGGAAAGACAGGGATGTTGAACTCG

upper sequence: GRMZM2G027311_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT3G18210.1 (Arabidopsis thaliana), 3'ss of exon 4

----gttgtctgaatgacttctatgttgtcacatatatcgatcactttatttcagttgtttct--cattaatctta------tgctctgggt----tgatctttagTTCTTTATCCTGAGGTTGGTGGAGGAACATTGGACTCCCATCACGCTTTTATTGTTGAATATGGGAAAGACAGGGATGTTGAACTAG
      | | |  |   |   ||  | |||  || ||| |   | | | ||| |  ||||       ||||   ||      | ||  |  |    || | |  |||  | |    ||| || ||||||| |||  ||||||| || || | |||| ||||||||||||||||||| |||||||||||  |||
gcaatatatttttaaatccattacatagtc-tat-tattggaaagtctgtttaatatgttcacagtgttaaaactaaaaagctacttcgaatcttttgttttgcagTATTCTTCAGTGATGTGGGTGGAGCAACTCTGGACTCTCACCATGGTTTTGTTGTTGAATATGGGAAAGATAGGGATGTTGATTTAG

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|67020949|gb|CO449698.1|CO449698

EST:     AGCTATGCTGAACCAGTTCATGGAACAGTTCATAGCTCCAATTTCTAAAG                         TTCTTTATCCTGAGGTTGGTGGAGGAACATTGGACTCCCATCACGCTTTTA
genomic: AGCTATGCTGAACCAGTTCATGGAACAGTTCATAGCTCCAATTTCTAAAGgttgtctgaa ... tgatctttagTTCTTTATCCTGAGGTTGGTGGAGGAACATTGGACTCCCATCACGCTTTTA

EST: gi|166610073|gb|EG162101.1|EG162101

EST:     CCAATTTCTAAAG                         TTCTTTATCCTGAGGTTGGTGGAGGAACATTGGACTCCCATCACGCTTTTA
genomic: CCAATTTCTAAAGgttgtctgaa ... tgatctttagTTCTTTATCCTGAGGTTGGTGGAGGAACATTGGACTCCCATCACGCTTTTA

EST: gi|76923272|gb|DV169406.1|DV169406

EST:     AGCTATGCTGAACCAGTTCATGGAACAGTTCATAGCTCCAATTTCTAAAG                         TTCTTTATCCTGAGGTTGGTGGAGGAACATTGGACTCCCATCACGCTTTTA
genomic: AGCTATGCTGAACCAGTTCATGGAACAGTTCATAGCTCCAATTTCTAAAGgttgtctgaa ... tgatctttagTTCTTTATCCTGAGGTTGGTGGAGGAACATTGGACTCCCATCACGCTTTTA

EST: gi|91875688|gb|EB405645.1|EB405645

EST:     AGCTATGCTGAACCAGTTCATGGAACAGTTCATAGCTCCAATTTCTAAAG                         TTCTTTATCCTGAGGGTGGTGGAGGAACATTGGACTCCCATCACGCTTT
genomic: AGCTATGCTGAACCAGTTCATGGAACAGTTCATAGCTCCAATTTCTAAAGgttgtctgaa ... tgatctttagTTCTTTATCCTGAGGTTGGTGGAGGAACATTGGACTCCCATCACGCTTT

EST: gi|76912282|gb|DV164655.1|DV164655

EST:     AGCTATGCTGAACCAGTTCATGGAACAGTTCATAGCTCCAATTTCTAAAG                         TTCTTTATCCTGAGGTTGGTGGAGGAACATTGGACT
genomic: AGCTATGCTGAACCAGTTCATGGAACAGTTCATAGCTCCAATTTCTAAAGgttgtctgaa ... tgatctttagTTCTTTATCCTGAGGTTGGTGGAGGAACATTGGACT

EST: gi|78106665|gb|DV525083.1|DV525083

EST:     GCTATGCTGAACCAGTTCATGGAACAGTTCATAGCTCCAATTTCNTAA-G                         TTCTTTATCCTGAGGTTGGTGGAGGAACATTGGACTCCCATCACGCTTTT
genomic: GCTATGCTGAACCAGTTCATGGAACAGTTCATAGCTCCAATTTC-TAAAGgttgtctgaa ... tgatctttagTTCTTTATCCTGAGGTTGGTGGAGGAACATTGGACTCCCATCACGCTTTT

EST: gi|31355557|gb|CD439914.1|CD439914

EST:     AGCTATGCTGAACCAGTTCATGGAACAGTTCATAGCTCCAATTTCTAAAG                         TTCTTTATCCTGAGGTTGGTGGAGGAACATTGGACTCCCATCACGCTTTTA
genomic: AGCTATGCTGAACCAGTTCATGGAACAGTTCATAGCTCCAATTTCTAAAGgttgtctgaa ... tgatctttagTTCTTTATCCTGAGGTTGGTGGAGGAACATTGGACTCCCATCACGCTTTTA

EST: gi|78076294|gb|DV504728.1|DV504728

EST:     AGCTATGCTGAACCAGTTCATGGAACAGTTCATAGCTCCAATTTCTAAAG                         TTCTTTATCCTGAGGTTGGTGGAGGAACATTGGACTCCCATCACGCTTTTA
genomic: AGCTATGCTGAACCAGTTCATGGAACAGTTCATAGCTCCAATTTCTAAAGgttgtctgaa ... tgatctttagTTCTTTATCCTGAGGTTGGTGGAGGAACATTGGACTCCCATCACGCTTTTA

EST: gi|32850618|gb|CD990299.1|CD990299

EST:     AGCTATGCTGAACCAGTTCATGGAACAGTTCATAGCTCCAATTTCTAAAG                         TTCTTTATCCTGAGGTTGGTGGAGGAACATTGGACTCCCATCACGCTTTTA
genomic: AGCTATGCTGAACCAGTTCATGGAACAGTTCATAGCTCCAATTTCTAAAGgttgtctgaa ... tgatctttagTTCTTTATCCTGAGGTTGGTGGAGGAACATTGGACTCCCATCACGCTTTTA

EST: gi|149015102|gb|EE044860.2|EE044860

EST:     AGCTATGCTGAACCAGTTCATGGAACAGTTCATAGCTCCAATTTCTAAAG                         TTCTTTATCCTGAGGTTGGTGGAGGAACATTGGACTCCCATCACGCTTTTA
genomic: AGCTATGCTGAACCAGTTCATGGAACAGTTCATAGCTCCAATTTCTAAAGgttgtctgaa ... tgatctttagTTCTTTATCCTGAGGTTGGTGGAGGAACATTGGACTCCCATCACGCTTTTA

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: 197

CCTAATACAATGAACAAGTATGGTGCTGTCCTTGATGATTTTGGCCTGGAAGCTATGCTGAACCAGTTCATGGAACAGTTCATAGCTCCAATTTCTAAAGgttgtctgaa ... tgatctttagTTCTTTATCCTGAGGTTGGTGGAGGAACATTGGACTCCCATCACGCTTTTATTGTTGAATATGGGAAAGACAGGGATGTTGAACTAG

Block sizes: 47 (upstream exon), 44 (downstream exon)
Score: 122

Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 100

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 97

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

gatcactttatttcagttgtttctcattaatcttatgctctgggttgatctttagTTCTTTATCCTGAGGTTGGTGGAGGAACATTGGACTCCCATCACGCTTTTATTGTTGAATATGGGAAAGACAGGGATGTTGAACTAG