ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

TATTGGCTTGGCACACAGGGAGGAAGGTGATCTAGGTCCAGTTTATGGATTTCAATGGCGACACTTTGGTGCCGAgtaagcttacattcctttccttgagctgtatcttttttcttgttcatgttttctgataaagttgacatatctgacag

Basic information

species	Zea mays
transcript	GRMZM2G139880_T01
intron #	6
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G139880_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os11g29390.1 (Oryza sativa), 5'ss of exon 7

TATTGGCTTGGCACACAGGGAGGAAGGTGATCTAGGTCCAGTTTATGGATTTCAATGGCGACACTTTGGTGCCGAgtaagcttacattcctttccttga--------gctgtatcttttttcttgttcatgt---tttctga----taaagttgacatatctg--acag
| ||||||| ||||| ||||| |||||||||||||||||||||||||||||||||||||||||||||||||| ||||||| ||   |  |   |||  |        | |||| |  | |   ||| ||| |   | ||| |    ||| |   |  ||| ||  ||||
TGTTGGCTTAGCACATAGGGAAGAAGGTGATCTAGGTCCAGTTTATGGATTTCAATGGCGACACTTTGGTGCTGAgtaagtttttctctcgcccctacatacctatcgatgtaccaatctatctgtccatctaggtctctaaggactaaggactaactatttgtaacag

upper sequence: GRMZM2G139880_T01 (Zea mays), 5'ss of exon 6
lower sequence: AT4G34570.1 (Arabidopsis thaliana), 5'ss of exon 9

TATTGGCTTGGCACACAGGGAGGAAGGTGATCTAGGTCCAGTTTATGGATTTCAATGGCGACACTTTGGTGCCGAgtaagc--ttacattcctttccttgagctgtatcttttttcttgtt---catgttttctgataaagttgacatatctgacag---------
||||||  || |  | || ||||||||||| || || || |||||||||||||| ||| |||||||||||||  ||| ||    | |  || | ||  |   |  | |||   || | |     ||  |||     |  ||      | |    |           
TATTGGACTGACTGAGAGAGAGGAAGGTGACCTTGGACCCGTTTATGGATTTCAGTGGAGACACTTTGGTGCTAAgtcagtagcttctctcttatctcttgacactttctgagttttggcaaaacagatttctgtgtcgagacattttgttcatctctctctacag

upper sequence: GRMZM2G139880_T01 (Zea mays), 5'ss of exon 6
lower sequence: AT2G16370.1 (Arabidopsis thaliana), 5'ss of exon 7

TATTGGCTTGGCACACAGGGAGGAAGGTGATCTAGGTCCAGTTTATGGATTTCAATGGCGACACTTTGGTGCCGAgtaagcttacattcctttccttgagctgtatcttttttct-tgttc------atgttttctgataaag-----ttgacatatctgacag
||| ||| || || | || |||||||| || || || || || || ||||||||||||||||||||||||||  ||| || | || || |  | | |  | ||  | ||| |||| |||||      || | || || | ||      ||  | | | | ||||
TATCGGCCTGACAGAGAGAGAGGAAGGCGACCTTGGACCTGTATACGGATTTCAATGGCGACACTTTGGTGCTAAgtcag-taacttttcaatgcatatgttggttttttcttctctgttccgatggatttgttttggtgaaacatctttctcttgttttacag

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|84980638|gb|DW530987.1|DW530987

EST:     GGTGATCTAGGTCCAGTTTATGGATTTCAATGGCGGCACTTTGGTGCTGA                         ATACACTGACATGCATGCTGACTATACTGGAAAAGGCTTTGATCAGCTAAT
genomic: GGTGATCTAGGTCCAGTTTATGGATTTCAATGGCGACACTTTGGTGCCGAgtaagcttac ... tatctgacagATATACTGACATGCATGCTGACTATACTGGAAAAGGCTTTGATCAGCTAAT

EST: gi|32838087|gb|CD977765.1|CD977765

EST:     GGTGATCTAGGTCCAGTTTATGGATTTCAATGGCGACACTTTGGTGCTGA                         ATATACTGACATGCATGCTGACTATACTG
genomic: GGTGATCTAGGTCCAGTTTATGGATTTCAATGGCGACACTTTGGTGCCGAgtaagcttac ... tatctgacagATATACTGACATGCATGCTGACTATACTG

EST: gi|67012996|gb|CO441745.1|CO441745

EST:     GGTGATCTAGGTCCAGTTTATGGATTTCAATGGCGGCACTTTGGTGCTGA                         ATACACTGACATGCACGCTGACTATACTGGAAAAGGCTTTGATCAGCTAAT
genomic: GGTGATCTAGGTCCAGTTTATGGATTTCAATGGCGACACTTTGGTGCCGAgtaagcttac ... tatctgacagATATACTGACATGCATGCTGACTATACTGGAAAAGGCTTTGATCAGCTAAT

EST: gi|32930437|gb|CF035249.1|CF035249

EST:     GGTGATCTAGGTCCAGTTTATGGATTTCAATGGCGACACTTTGGTGCTGA                         ATATACTGACATGCATGCTGACTATACTGGAAAAGGCTTTGATCAGCTAAT
genomic: GGTGATCTAGGTCCAGTTTATGGATTTCAATGGCGACACTTTGGTGCCGAgtaagcttac ... tatctgacagATATACTGACATGCATGCTGACTATACTGGAAAAGGCTTTGATCAGCTAAT

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: 47 (upstream exon), 49 (downstream exon)
Score: 123

TATTGGCTTGGCACACAGGGAGGAAGGTGATCTAGGTCCAGTTTATGGATTTCAATGGCGACACTTTGGTGCCGAgtaagcttac ... tatctgacagATATACTGACATGCATGCTGACTATACTGGAAAAGGCTTTGATCAGCTAATGGATGTGATTGACAAGATTAAGAACAATCCTGATGACCGCCGAATAATT

Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 91

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 65