ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

AACCCAAGACTATCATGTTTTGGTCTGATGAAGAACAGCCGTGATGGAAAGAGCTACAGTACTAATTTGGCCTTCACGCCTCCTGAGTATCTTAAGACAGgtaaatgtgccacacgctagcaatagtatccatgaaacatttttgggaatgtgcctcttcatttgttttgaactgttatctgttctgcacctgcag

Basic information

species	Zea mays
transcript	GRMZM2G121826_T02
intron #	5
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G121826_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os03g61010.1 (Oryza sativa), 5'ss of exon 5

AACCCAAGACTATCATGTTTTGGTCTGATGAAGAACAGCCGTGATGGAAAGAGCTACAGTACTAATTTGGCCTTCACGCCTCCTGAGTATCTTAAGACAGgtaaatgtgccacacgctagcaatagtatccatgaaacatttttgggaatgtgcctcttcatttgttt-tgaactgttatctgttctgcacctgcag-----
||||| ||||| || || || |||||||||||||||||| | ||||| |||||||| ||||| |||||||| ||||||||||||||||| |||||||| ||||  |||    ||  | |||||   | |   ||  |  || |        ||  | || |||||||  ||     | ||    |  | || || |      
AACCCCAGACTGTCGTGCTTCGGTCTGATGAAGAACAGCAGGGATGGGAAGAGCTATAGTACCAATTTGGCTTTCACGCCTCCTGAGTACCTTAAGACTGgtatgtgttgtgcatacaagcaagtttttttctgtga-gttatgcatttcatgaatttt-atttgttaatgtttgatcatgaagtaaggacttgtaatatga

upper sequence: GRMZM2G121826_T01 (Zea mays), 5'ss of exon 5
lower sequence: PP1S122_66V6.1 (Physcomitrella patens), 5'ss of exon 5

AACCCAAGACTATCATGTTTTGGTCTGATGAAGAACAGCCGTGATGGAAAGAGCTACAGTACTAATTTGGCCTTCACGCCTCCTGAGTATCTTAAGACAGgta--aatgtgccacacgcta-gcaatagtatccatgaaacatttttgggaatgtgcctcttcatttgt----tttgaactgttatctgttctgcacct-gcag
 | ||  | || || |||||||| || ||||||||||| || |||||||| ||||| ||||| ||| |||||| ||| || ||||| ||  | |  || ||||   |  | |   | | |  |    | | |  ||  |||| ||| |  | |||  || |  |||||     ||   ||  || |  || || ||  | ||||
GATCCGCGCCTCTCTTGTTTTGGCCTCATGAAGAACAGTCGCGATGGAAAAAGCTATAGTACCAATCTGGCCTACACTCCCCCTGAATACTTAAGAACTGgtaccgaaatcctgaatgttttgttggattgtttattgaacaattt-gttattgttactttcaatttgcatcattctgacgattcttggtacttcattttgcag

upper sequence: GRMZM2G121826_T01 (Zea mays), 5'ss of exon 5
lower sequence: PP1S156_133V6.1 (Physcomitrella patens), 5'ss of exon 5

AACCCAAGACTATCATGTTTTGGTCTGATGAAGAACAGCCGTGATGGAAAGAGCTACAGTACTAATTTGGCCTTCACGCCTCCTGAGTATCTTAAGACAGgta----aatgtgccacacgctagcaatagtatccatgaaacatttttgggaatgtgcctcttcatttgttttgaactgttatctgttctgcacctgcag-------------------------------------------
 ||||| | || || |||||||| || |||||||||||| | ||||| || |||||||| || ||| |||| | ||| |||||||||||  | |  |||||||    |  ||  | | |  |    || | ||   |||   |    ||| |||  ||   |||  || | || ||    |   ||         ||||                                            
GACCCACGTCTCTCCTGTTTTGGGCTCATGAAGAACAGCAGAGATGGGAAAAGCTACAGCACCAATCTGGCTTACACTCCTCCTGAGTACTTAAGAACAGgtatcccacggtttccctctttctggatcgaatatttgagcaacc--tggaaattagcaatttctattatgttaaatgtatgcatgcataatgtatgcatgcttctctttggtacgtgacaaatgtcataagagggtttgcag

upper sequence: GRMZM2G121826_T01 (Zea mays), 5'ss of exon 5
lower sequence: PP1S9_348V6.1 (Physcomitrella patens), 5'ss of exon 5

AACCCAAGACTATCATGTTTTGGTCTGATGAAGAACAGCCGTGATGGAAAGAGCTACAGTACTAATTTGGCCTTCACGCCTCCTGAGTATCTTAAGACAGgtaaatgt-------gccacacgctagcaatagtatccatgaaacatttttgggaatgtgcctcttcatttgttttgaactgttatctgtt--ctgcacctgcag-------------------------------------------------------------------
 ||||| | || || |||||||| || |||||||||||| | |||||||| |||||||| || |||||||| | ||| |||||||||||  | |  |||||| ||          | ||    || | || ||  |    |  | ||  | ||  |  |   | ||  | |   |   |  | | |    |  ||    |    |                                                                   
GACCCACGTCTCTCCTGTTTTGGGCTCATGAAGAACAGCAGAGATGGAAAAAGCTACAGCACCAATTTGGCTTACACTCCTCCTGAGTACTTGAGAACAGgttaacaactttttgggcatcttctgggaagagcttgtgaggga-atggtgggttagctatatttttgtcttcgtaagatcgatgttcactgcctaagtcaatcggtcgaggaaccctggaactcccgtgattctgtttggtcagtgacggtcatttttcgatattttgcag

upper sequence: GRMZM2G121826_T01 (Zea mays), 5'ss of exon 5
lower sequence: PP1S178_86V6.1 (Physcomitrella patens), 5'ss of exon 5

------AACCCAAGACTATCATGTTTTGGTCTGATGAAGAACAGCCGTGATGGAAAGAGCTACAGTACTAATTTGGCCTTCACGCCTCC-TGAGTATCTTAAGACAGgtaaatgtgccacacgctagcaatagtatccatgaaa-------catttttgggaatgtgcct----cttcatttgttttgaactgttatctgttctgcacctgcag------------------------------------
       | ||| | || || || || || || |||||||||||||  |||||||||||||||||||| || ||||| | ||| || || ||||||  | |  || |||||    | |  | ||| |  |  ||||    | ||       |||| ||  | |  | ||      | |     ||   | | |   |   ||  | |     |                                     
GAGGGGGATCCACGTCTCTCCTGCTTCGGCCTCATGAAGAACAGCCAAGATGGAAAGAGCTACAgtaccaacttggcatacacccccccatgagtacttaagaactggtaacgaagtctgaagcttggtaatgtatttgcgcaattctggacattattacggacctacccaaaattaccaacattcaaagcagccctggatttagtatgcttactttggattcctgagattcttgtattcaaatttgcag

upper sequence: GRMZM2G121826_T01 (Zea mays), 5'ss of exon 5
lower sequence: EFJ20301 (Selaginella moellendorffii), 5'ss of exon 4

AACCCAAGACTATCATGTTTTGGTCTGATGAAGAACAGCCGTGATGGAAAGAGCTACAGTACTAATTTGGCCTTCACGCCTCCTGAGTATCTTAAGACAGgtaaatgtgccacacgctagcaatagtatccatgaaacatttttgggaatgtgcctcttcatttgttttgaactgttatctgttctgcacctgcag
 | ||  | || || ||||| |||||||||||||||||||| || || |||||||| || || || ||||| |  || |||||||| ||  |    |||||||||  |  |   |  | |  |   |    ||  ||   |||      | |   | | ||                                   
GATCCGCGCCTCTCTTGTTTCGGTCTGATGAAGAACAGCCGAGACGGCAAGAGCTATAGCACGAACTTGGCATATACACCTCCTGAATACTTGCGAACAGgtaaagctctcgtgcctttgtcaccttgcgtattcaaagcttt----gttttctgtttgcag----------------------------------

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|148945740|gb|EC891020.2|EC891020

EST:     GAGCTACAGTACTAATTTGGCCTTCACGCCTCCTGAGTATCTTAAGACAG                         GCAGAGTAAGTCCTGAGAGTGTGGTTTACAGTTTTGGCACTGTCTTGCTTG
genomic: GAGCTACAGTACTAATTTGGCCTTCACGCCTCCTGAGTATCTTAAGACAGgtaaatgtgc ... gcacctgcagGCAGAGTAAGTCCTGAGAGTGTGGTTTACAGTTTTGGCACTGTCTTGCTTG

EST: gi|148982427|gb|EE028311.2|EE028311

EST:     GAGCTACAGTACTAATTTGGCCTTCACGCCTCCTGAGTATCTTAAGACAG                         GCAGAGTAAGTCCTGAGAGTGTGGTTTACAGTTTTGGCACTGTCTTGCTTG
genomic: GAGCTACAGTACTAATTTGGCCTTCACGCCTCCTGAGTATCTTAAGACAGgtaaatgtgc ... gcacctgcagGCAGAGTAAGTCCTGAGAGTGTGGTTTACAGTTTTGGCACTGTCTTGCTTG

EST: gi|149103589|gb|EE288989.2|EE288989

EST:     GAGCTACAGTACTAATTTGGCCTTCACGCCTCCTGAGTATCTTAAGACAG                         GCAGAGTAAGTCCTGAGAGTGTGGTTTACAGTTTTGGCACTGTCTTGCTTG
genomic: GAGCTACAGTACTAATTTGGCCTTCACGCCTCCTGAGTATCTTAAGACAGgtaaatgtgc ... gcacctgcagGCAGAGTAAGTCCTGAGAGTGTGGTTTACAGTTTTGGCACTGTCTTGCTTG

EST: gi|71302365|gb|DR787300.1|DR787300

EST:     GAGCTACAGTACTAATTTGGCCTTCACGCCTCCTGAGTATCTTAAGACAG                         GCAGAGTAAGTCCTGAGAGTGTGGTTTACGGTTTTGGCACTGTCTTGCTT
genomic: GAGCTACAGTACTAATTTGGCCTTCACGCCTCCTGAGTATCTTAAGACAGgtaaatgtgc ... gcacctgcagGCAGAGTAAGTCCTGAGAGTGTGGTTTACAGTTTTGGCACTGTCTTGCTT

EST: gi|9952364|gb|BE638947.1|BE638947

EST:     GAGCTACAGTACTAATTTGGCCTTCACGCCTCCTGAGTATCTTAAGACAG                         GCAGAGTAAGTCCTGAGA
genomic: GAGCTACAGTACTAATTTGGCCTTCACGCCTCCTGAGTATCTTAAGACAGgtaaatgtgc ... gcacctgcagGCAGAGTAAGTCCTGAGA

EST: gi|149012049|gb|EE042465.2|EE042465

EST:     GAGCTACAGTACTAATTTGGCCTTCCCGCCTCCTGAGTATCTTAAGACAG                         GCAGAGTAAGTCCTGAGA
genomic: GAGCTACAGTACTAATTTGGCCTTCACGCCTCCTGAGTATCTTAAGACAGgtaaatgtgc ... gcacctgcagGCAGAGTAAGTCCTGAGA

EST: gi|9952536|gb|BE639119.1|BE639119

EST:     GAGCTACAGTACTAATTTGGCCTTCACGCCTCCTGAGTATCTTAAGACAG                         GCAGAGTAAGTCCTGAGAGTGTGGTTTACAGTTTTGGCACTGTCTTGCTTG
genomic: GAGCTACAGTACTAATTTGGCCTTCACGCCTCCTGAGTATCTTAAGACAGgtaaatgtgc ... gcacctgcagGCAGAGTAAGTCCTGAGAGTGTGGTTTACAGTTTTGGCACTGTCTTGCTTG

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: 128

AACCCAAGACTATCATGTTTTGGTCTGATGAAGAACAGCCGTGATGGAAAGAGCTACAGTACTAATTTGGCCTTCACGCCTCCTGAGTATCTTAAGACAGgtaaatgtgc ... gcacctgcagGCAGAGTAAGTCCTGAGAGTGTGGTTTACAGTTTTGGCACTGTCTTGCTTGATCTCCTGAGTGGAAAGCACATTCCACCAAGTCAT

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 26

Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 24