ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

ATCTAGCGCAGAATAGATATTTCGAGGATGAGGCATTTATCGGGTACCTCAAGTATCTAAAATACTGGCAGCGACCAGAGTATATCAAATACATAATgtgagtgataccatattcagtggttttttctgcaacagaggaaatggcttgctcattgtttttgctgatgatgcag

Basic information

species	Zea mays
transcript	GRMZM2G139683_T03
intron #	3
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G139683_T03 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os10g41450.1 (Oryza sativa), 5'ss of exon 3

ATCTAGCGCAGAATAGATATTTCGAGGATGAGGCATTTATCGGGTACCTCAAGTATCTAAAATACTGGCAGCGACCAGAGTATATCAAATACATAATgtgagtgataccata-ttcagtggttttttctgcaaca----------gaggaaatggcttgctcattgtttttgctgatgatgcag
||||||| |||||||| || || ||||||||||||||||||||||| ||||||||||| |||||||||||||| || ||||| |||||||||||||||||||||     ||| || ||   | ||| ||   |            ||  |||| ||||| |||   |  ||| || |  || ||
ATCTAGCACAGAATAGGTACTTTGAGGATGAGGCATTTATCGGGTATCTCAAGTATCTCAAATACTGGCAGCGTCCGGAGTACATCAAATACATAATgtgagtggccgtataatttagatctgtttgctagtaggtgcttgctgtgacaaaatagcttggtcacactggttgttgtttgtgtag

upper sequence: GRMZM2G139683_T03 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os07g07020.2 (Oryza sativa), 5'ss of exon 2

ATCTAGCGCAGAATAGATATTTCGAGGATGAGGCATTTATCGGGTACCTCAAGTATCTAAAATACTGGCAGCGACCAGAGTATATCAAATACATAATgtgagtgataccatattcagtggttttttctgcaacagag-------------gaaatggctt-gctcattgtttttgctgatgatgcag
||||||||||||| ||||| || ||||||||||| |||||||| || ||||||||||| || || |||||||| || ||||| ||||| ||||||||||| |||   | ||| |   | | ||| |||||||    |             |||||  ||| | |||| ||  |||||||||||||||
ATCTAGCGCAGAACAGATACTTTGAGGATGAGGCGTTTATCGGTTATCTCAAGTATCTCAAGTATTGGCAGCGTCCGGAGTACATCAAGTACATAATgtgtgtggccctataatt--tagatttatctgcaagtaggtgcctgctgtgacgaaatacctttgttcatagtggttgctgatgatgcag

upper sequence: GRMZM2G139683_T03 (Zea mays), 5'ss of exon 3
lower sequence: AT5G19910.1 (Arabidopsis thaliana), 5'ss of exon 3

ATCTAGCGCAGAATAGATATTTCGAGGATGAGGCATTTATCGGGTACCTCAAGTATCTAAAATACTGGCAGCGACCAGAGTATATCAAATACATAATgtgagt---gataccatattca------gtggtttt------ttctgcaacagaggaaatggcttgctcattgtttt---tgctgatgatgcag
| || || |||||| | ||||| || ||||| |||||||| || ||| | ||||||||  |||||||||||||||||||||| ||||| | ||| |||| |||    ||| | |||  |      || || ||      |  ||  |  |     ||    |     | ||||    || |  || | |||
ACCTGGCACAGAATCGGTATTTTGAAGATGAAGCATTTATTGGATACTTGAAGTATCTTCAATACTGGCAGCGACCAGAGTACATCAAGTTCATTATgtaagttggaatatcttatggaattggtgtagtcttgtagagtcttgtgaaggtttggataatatatctttggtttcctatgttcttgttacag

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|211343281|gb|FL146112.1|FL146112

EST:     CTCAAGTATCTAAAATACTGGCAGCGACCAGAGTATATCAAATACATAAT                         GTATCCACACTGCCTTTTCTTTCTTGAGCTTCTCCAAAAT
genomic: CTCAAGTATCTAAAATACTGGCAGCGACCAGAGTATATCAAATACATAATgtgagtgata ... gatgatgcagGTATCCACACTGCCTTTTCTTTCTTGAGCTTCTCCAAAAT

EST: gi|211340893|gb|FL146102.1|FL146102

EST:     CTCAAGTATCTAAAATACTGGCAGCGACCAGAGTATATCAAATACATAAT                         GTATCCACACTGCCTTTTCTTTCTTGAGCTTCTCCAAAATGCCAATT
genomic: CTCAAGTATCTAAAATACTGGCAGCGACCAGAGTATATCAAATACATAATgtgagtgata ... gatgatgcagGTATCCACACTGCCTTTTCTTTCTTGAGCTTCTCCAAAATGCCAATT

EST: gi|211343280|gb|FL146111.1|FL146111

EST:     CTCAAGTATCTAADATACTGGCAGCGACCAGAGTATATCAWATACATAAT                         GTATCCACACTGCCTTTTCTTTCTTGAGCTTCT
genomic: CTCAAGTATCTAAAATACTGGCAGCGACCAGAGTATATCAAATACATAATgtgagtgata ... gatgatgcagGTATCCACACTGCCTTTTCTTTCTTGAGCTTCT

EST: gi|76934686|gb|DV173976.1|DV173976

EST:     CTCAAGTATCTAAAATACTGGCAGCGACCAGAGTATATCAAATACATAAT                         GTATCCACACTGCCTTTTCTTTCTTGAGCTTCTCCAAAATGCCAATTTCCG
genomic: CTCAAGTATCTAAAATACTGGCAGCGACCAGAGTATATCAAATACATAATgtgagtgata ... gatgatgcagGTATCCACACTGCCTTTTCTTTCTTGAGCTTCTCCAAAATGCCAATTTCCG

EST: gi|211343276|gb|FL146107.1|FL146107

EST:     CTCAAGTATCTAAAATACTGGCAGCGACCAGAGTATATCAAATACATAAT                         GTATCCACACTGCCTTTTCTTTCTTGAGCTTCTCCAAAATGCCAATTTCCG
genomic: CTCAAGTATCTAAAATACTGGCAGCGACCAGAGTATATCAAATACATAATgtgagtgata ... gatgatgcagGTATCCACACTGCCTTTTCTTTCTTGAGCTTCTCCAAAATGCCAATTTCCG

EST: gi|28910217|gb|CB331329.1|CB331329

EST:     CTCAAGTATCTAAAATACTGGCAGCGACCAGAGTATATCAAATACATAAT                         GTATCCACACTGCCTTTTCTTTCTTGAGCTTCTCCAAAATGCCAATTTCCG
genomic: CTCAAGTATCTAAAATACTGGCAGCGACCAGAGTATATCAAATACATAATgtgagtgata ... gatgatgcagGTATCCACACTGCCTTTTCTTTCTTGAGCTTCTCCAAAATGCCAATTTCCG

EST: gi|26559121|gb|CA831356.1|CA831356

EST:     CTCAAGTATCTAAAATACTGGCAGCGACCAGAGTATATCAAATACATAAT                         GTATCCACACTGCCTTTTCTTTCTTGAGCTTCTCCAAAATGCCAATTTCCG
genomic: CTCAAGTATCTAAAATACTGGCAGCGACCAGAGTATATCAAATACATAATgtgagtgata ... gatgatgcagGTATCCACACTGCCTTTTCTTTCTTGAGCTTCTCCAAAATGCCAATTTCCG

EST: gi|211343275|gb|FL146106.1|FL146106

EST:     CTCAAGTATCTAAAATACTGGCAGCGACCAGAGTATATCAAATACATAAT                         GTATCCACACTGCCTTTTCTTTCTTGAGCTTCTCC
genomic: CTCAAGTATCTAAAATACTGGCAGCGACCAGAGTATATCAAATACATAATgtgagtgata ... gatgatgcagGTATCCACACTGCCTTTTCTTTCTTGAGCTTCTCC

EST: gi|87157028|gb|DY401817.1|DY401817

EST:     CTCAAGTATCTAAAATACTGGCAGCGACCAGAGTATATCAAATACATAAT                         GTATCCACACTGCCTTTTCTTTCTTGAGCTTCTCCAAAATGCCAATTTCCG
genomic: CTCAAGTATCTAAAATACTGGCAGCGACCAGAGTATATCAAATACATAATgtgagtgata ... gatgatgcagGTATCCACACTGCCTTTTCTTTCTTGAGCTTCTCCAAAATGCCAATTTCCG

EST: gi|22521504|gb|BU080315.1|BU080315

EST:     CTCAAGTATCTAAAATACTGGCAGCGACCAGAGTATATCAAATACATAAT                         GTATCCACACTGCCTTTTCTTTCTTGAGCTTCTCCAAAATGCCAATTTCCG
genomic: CTCAAGTATCTAAAATACTGGCAGCGACCAGAGTATATCAAATACATAATgtgagtgata ... gatgatgcagGTATCCACACTGCCTTTTCTTTCTTGAGCTTCTCCAAAATGCCAATTTCCG

EST: gi|211340894|gb|FL146103.1|FL146103

EST:     CTCAAGTATCTAAAATACTGGCAGCGACCAGAGTATATCAAATACATAAT                         GTATCCACACTGCCTTTTCTTTCTTGAGCTTCTCCAAAATGCCAATTTCCG
genomic: CTCAAGTATCTAAAATACTGGCAGCGACCAGAGTATATCAAATACATAATgtgagtgata ... gatgatgcagGTATCCACACTGCCTTTTCTTTCTTGAGCTTCTCCAAAATGCCAATTTCCG

EST: gi|60352751|gb|DN219724.1|DN219724

EST:     CTCAAGTATCTAAAATACTGGCAGCGACCAGAGTATATCAAATACATAAT                         GTATCCACACTGCCTTTTCTTTCTTGAGCTTCTCCAAAATGCCAATTTCCG
genomic: CTCAAGTATCTAAAATACTGGCAGCGACCAGAGTATATCAAATACATAATgtgagtgata ... gatgatgcagGTATCCACACTGCCTTTTCTTTCTTGAGCTTCTCCAAAATGCCAATTTCCG

EST: gi|211343278|gb|FL146109.1|FL146109

EST:     TCAAGTATCTAAAATACTGGCAGCGACCAWGAGTATATCAAATACATAAT                         GTATCCACACTGCCTTTTCTTTCTTGAGCTTCTCCAAA
genomic: TCAAGTATCTAAAATACTGGCAGCGACCA-GAGTATATCAAATACATAATgtgagtgata ... gatgatgcagGTATCCACACTGCCTTTTCTTTCTTGAGCTTCTCCAAA

EST: gi|211340890|gb|FL146099.1|FL146099

EST:     CTCAAGTATCTAAAATACTGGCAGCGACCAGAGTATATCAAATACATAAT                         GTATCCACACTGCCTTTTCTTTCTTGAGCTTCTCCAAAATGCCAATTTCCG
genomic: CTCAAGTATCTAAAATACTGGCAGCGACCAGAGTATATCAAATACATAATgtgagtgata ... gatgatgcagGTATCCACACTGCCTTTTCTTTCTTGAGCTTCTCCAAAATGCCAATTTCCG

EST: gi|71765862|gb|DR963799.1|DR963799

EST:     CTCAAGTATCTAAAATACTGGCAGCGACCAGAGTATATCAAATACATAAT                         GTATCCACACTGCCTTTTCTTTCTTGAGCTTCTCCAAAATGCCAATTTCCG
genomic: CTCAAGTATCTAAAATACTGGCAGCGACCAGAGTATATCAAATACATAATgtgagtgata ... gatgatgcagGTATCCACACTGCCTTTTCTTTCTTGAGCTTCTCCAAAATGCCAATTTCCG

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: 81

ATCTAGCGCAGAATAGATATTTCGAGGATGAGGCATTTATCGGGTACCTCAAGTATCTAAAATACTGGCAGCGACCAGAGTATATCAAATACATAATgtgagtgata ... gatgatgcagGTATCCACACTGCCTTTTCTTTCTTGAGCTTCTCCAAAATGCCAATTTCCGAAATGCAATGGCACATCCAACAAACAAG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 53

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 78