ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

CACAAACTACATTACTGATATCATCTGCAAGCGTGCAGATCTTGGTTACAACTATGGTGTTATCCTTATACCAGAAGGCCTGATTGATTTCATCCCAGAGgtttgactctatgttctgtgactgtgttacccgtagaacatattactgacataactccttttcttttgaag

Basic information

species	Zea mays
transcript	GRMZM2G143862_T01
intron #	2
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G143862_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os06g13810.1 (Oryza sativa), 5'ss of exon 9

CACAAACTACATTACTGATATCATCTGCAAGCGTGCAGATCTTGGTTACAACTATGGTGTTATCCTTATACCAGAAGGCCTGATTGATTTCATCCCAGAGgtttgac--tctatgttc---tgtgact-gtgttacccgtagaacatattactgacataactccttttcttttgaag
|||  |||||||||| || ||  |||||||||||||||| |||||||||||||||||||| |||||||| ||||| || ||||||||||||||||||||||||||||  |||   |||   ||||| | |||||  |          ||||||||  | | ||  |||||||   ||
CACCGACTACATTACCGACATTGTCTGCAAGCGTGCAGAACTTGGTTACAACTATGGTGTGATCCTTATCCCAGAGGGTCTGATTGATTTCATCCCAGAGgtttgacaatcttcattcacctgtgatttgtgttgtc-acgatttgcattactgatttcattctgtttctttcctag

upper sequence: GRMZM2G143862_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA09G01050.1 (Glycine max), 5'ss of exon 9

CACAAACTACATTACTGATATCATCTGCAAGCGTGCAGATCTTGGTTACAACTATGGTGTTATCCTTATACCAGAAGGCCTGATTGATTTCATCCCAGAGgt--ttgactctatg------ttctgtgactgtgttacccgtagaacatattactgacata-actccttttcttttgaag---------------------------------------------------------------------
|||  |||| ||    ||  |  | || ||  | || ||  ||  ||||||||||||||| || ||||| || ||||| || ||||||||||| || |||||   |  | || ||      ||     | | | ||||  | |   |   |||   || |  | |  | || |  ||  |                                                                     
CACTGACTATATCGTAGACGTTGTTTGTAAAAGAGCTGAAATTAATTACAACTATGGTGTCATTCTTATCCCTGAAGGTCTAATTGATTTCATACCTGAGgtatctatcactttgcacagttttcacaatttttttacttgcatttccctttatgcacttggaattatattttagtgctgttcatgtacaaccagtatgaatacacttctgatgatactcatttgtacttggtattgtgctatatgcag

upper sequence: GRMZM2G143862_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA15G11890.1 (Glycine max), 5'ss of exon 9

CACAAACTACATTACTGATATCATCTGCAAGCGTGCAGATCTTGGTTACAACTATGGTGTTATCCTTATACCAGAAGGCCTGATTGATTTCATCCCAGAGgtttg----actctatgttct-----gtgactgtgttacccgtagaacatattactgacataac-tccttttcttttgaag---------------------------------------------------------------------
|||| |||| ||    ||| |  | || ||  | || ||  ||  |||||| ||||||||||| ||||| || ||||| || ||||||||||| || ||||| |     ||| |    | |      | | | | ||||| ||    |    |    || |    |  | || |  ||  |                                                                     
CACAGACTATATCGTAGATGTTGTTTGTAAAAGAGCTGAAATTAATTACAATTATGGTGTTATTCTTATCCCCGAAGGTCTAATTGATTTCATACCTGAGgtatctatcactttgcagttttcacaattatttttttacctgtgtttccccctctgcacttgggattatgttttagtgttgttcatgtacaacctgtatgaatacacttctgatgatactcatttgtacttggtattgtgctatatgcag

upper sequence: GRMZM2G143862_T01 (Zea mays), 5'ss of exon 2
lower sequence: AT1G12000.1 (Arabidopsis thaliana), 5'ss of exon 9

CACAAACTACATTACTGATATCATCTGCAAGCGTGCAGATCTTGGTTACAACTATGGTGTTATCCTTATACCAGAAGGCCTGATTGATTTCATCCCAGAGgtttgactctat-gttctgtgactgtgttacccgtagaacatattactgacataactccttttctt--ttgaag--------------------------
|||| |||||||    ||| | |||||||| ||||| || |||||||||||||| ||||| || || || |||||||| ||||| || || || || ||||| ||     || ||      |  |  |   |        |    | | | |||| |  | |||||   ||| |                          
CACAGACTACATGGTGGATGTTATCTGCAAACGTGCTGAACTTGGTTACAACTACGGTGTCATACTGATTCCAGAAGGTCTGATCGACTTTATTCCTGAGgtgtgttgtcattgtaaaaaaatagaatctactacttttaaaccgattaatataattgttcttcttaactgatgattaattttatttcatgacttctcag

upper sequence: GRMZM2G143862_T01 (Zea mays), 5'ss of exon 2
lower sequence: Vv10s0116g00360.t01 (Vitis vinifera), 5'ss of exon 9

CACAAACTACATTACTGATATCATCTGCAAGCGTGCAGATCTTGGTTACAACTATGGTGTTATCCTTATACCAGAAGGCCTGATTGATTTCATCCCAGAGgtttgactctatgttctgtgactgtgttacccgtagaacatattactgac-----ataactccttttcttttgaag---------------------------
 ||| ||||||||  |||| |  ||||||| |||||||| ||||||||||||||||||||||| ||||| ||||||||||| ||||||||||| || ||||| | |   |   || |  ||||   |||    ||   | | ||  || |      | | |   | || ||| |||                           
TACAGACTACATTGTTGATGTTGTCTGCAAACGTGCAGAACTTGGTTACAACTATGGTGTTATACTTATTCCAGAAGGCCTTATTGATTTCATACCTGAGgtataatattg-attataagacttatttatt--taacccttttttttgtcctcttgtgaatgggtatccttttaagcaaacttgtcttgctttttttcaagtt

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|211507305|gb|FK969872.1|FK969872

EST:     ACTATGGTGTTATCCTTATACCAGAAGGCCTGATTGATTTCATCCCAGAG                         GTTCAAAAACTCATCGCGGAATTGAATGAAATTTTAGCACATGATGTTGTT
genomic: ACTATGGTGTTATCCTTATACCAGAAGGCCTGATTGATTTCATCCCAGAGgtttgactct ... tcttttgaagGTTCAAAAACTCATCGCGGAATTGAATGAAATTTTAGCACATGATGTTGTT

EST: gi|32932722|gb|CF037534.1|CF037534

EST:     ACTATGGTGTTATCCTTATACCAGAAGGCCTGATTGATTTCATCCCAGAG                         GTTCAAAAACTCATCGCGGAATTGAATGAAATTTTAGCACATGATGTTGTT
genomic: ACTATGGTGTTATCCTTATACCAGAAGGCCTGATTGATTTCATCCCAGAGgtttgactct ... tcttttgaagGTTCAAAAACTCATCGCGGAATTGAATGAAATTTTAGCACATGATGTTGTT

EST: gi|211507302|gb|FK969869.1|FK969869

EST:     ACTATGGTGTTATCCTTATACCAGAAGGCCTGATTGATTTCATCCCAGAG                         GTTCAAAAACTCATCGCGGAATTGAATGAAATTTTAGCACATGATGTTGTT
genomic: ACTATGGTGTTATCCTTATACCAGAAGGCCTGATTGATTTCATCCCAGAGgtttgactct ... tcttttgaagGTTCAAAAACTCATCGCGGAATTGAATGAAATTTTAGCACATGATGTTGTT

EST: gi|67015451|gb|CO444200.1|CO444200

EST:     ACTATGGTGTTATCCTTATACCAGAAGGCCTGATTGATTTCATCCCAGAG                         GTTCAAAAACTCATCGCGGAATTGAATGAAATTTTAGCACATGATGTTGTT
genomic: ACTATGGTGTTATCCTTATACCAGAAGGCCTGATTGATTTCATCCCAGAGgtttgactct ... tcttttgaagGTTCAAAAACTCATCGCGGAATTGAATGAAATTTTAGCACATGATGTTGTT

EST: gi|211182047|gb|FL030523.1|FL030523

EST:     ACTATGGTGTTATCCTTATACCAGAAGGCCTGATTGATTTCATCCCAGAG                         GTTCAAAAACTCATCGCGGAATTGAATGAAATTTTAGCACATGATGTTGTT
genomic: ACTATGGTGTTATCCTTATACCAGAAGGCCTGATTGATTTCATCCCAGAGgtttgactct ... tcttttgaagGTTCAAAAACTCATCGCGGAATTGAATGAAATTTTAGCACATGATGTTGTT

EST: gi|211507300|gb|FK969867.1|FK969867

EST:     ACTATGGTGTTATCCTTATACCAGAAGGCCTGATTGATTTCATCCCAGAG                         GTTCAAAAACTCATCGCGGAATTGAATGAAATTTTAGCACATGATGTTGTT
genomic: ACTATGGTGTTATCCTTATACCAGAAGGCCTGATTGATTTCATCCCAGAGgtttgactct ... tcttttgaagGTTCAAAAACTCATCGCGGAATTGAATGAAATTTTAGCACATGATGTTGTT

EST: gi|32930610|gb|CF035422.1|CF035422

EST:     ACTATGGTGTTATCCTTATACCAGAAGGCCTGATTGATTTCATCCCAGAG                         GTTCAAAAACTCATCGCGGAATTGAATGAAATTTTAGCACATGATGTTGTT
genomic: ACTATGGTGTTATCCTTATACCAGAAGGCCTGATTGATTTCATCCCAGAGgtttgactct ... tcttttgaagGTTCAAAAACTCATCGCGGAATTGAATGAAATTTTAGCACATGATGTTGTT

EST: gi|211507306|gb|FK969873.1|FK969873

EST:     ACTATGGTGTTATCCTTATACCAGAAGGCCTGATTGATTTCATCCCAGAG                         GTTCAAAAACTCATCGCGGAATTGAATGAAATTTTAGCACATGATGTTGTT
genomic: ACTATGGTGTTATCCTTATACCAGAAGGCCTGATTGATTTCATCCCAGAGgtttgactct ... tcttttgaagGTTCAAAAACTCATCGCGGAATTGAATGAAATTTTAGCACATGATGTTGTT

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), 45 (downstream exon)
Score: 264

CACAAACTACATTACTGATATCATCTGCAAGCGTGCAGATCTTGGTTACAACTATGGTGTTATCCTTATACCAGAAGGCCTGATTGATTTCATCCCAGAGgtttgactct ... tcttttgaagGTTCAAAAACTCATCGCGGAATTGAATGAAATTTTAGCACATGATGTTGTTGATGAGGCAGGGGCCTGGAAAAGCAAGCTTCAGGCTGAATCAAGGGAGC

Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 290

Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 389