ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GAGAAGATGACCCAGATCATGTTCGAGACCTTCAACACCCCGGCTATGTACGTCGCCATCCAGGCCGTGCTCTCTCTGTATGCCAGTGGCCGTACCACAGgtgagctgattccgttctctgcttaacaatttccaaatccgatttgctcctgcagtccgttatctctaatatctgtggcttcccctctctcag

Basic information

species	Zea mays
transcript	GRMZM2G152328_T02
intron #	2
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G152328_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os03g50885.1 (Oryza sativa), 5'ss of exon 2

GAGAAGATGACCCAGATCATGTTCGAGACCTTCAACACCCCGGCTATGTACGTCGCCATCCAGGCCGTGCTCTCTCTGTATGCCAGTGGCCGTACCACAGgtgagctgattccgttctctgcttaacaatt-tccaaatccgatttgctcctgcagtccgttatctctaatatctgtggcttcccctctctcag-------
||||||||||||||||||||||| ||||||||||||||||| |||||||||||||||||||||||||| |||||||||||||||||||| ||||||||||||||||  ||||    ||   || ||    | |    ||    |||  |  ||   | |   || |  |  |  | | | |   |     |||        
GAGAAGATGACCCAGATCATGTTTGAGACCTTCAACACCCCTGCTATGTACGTCGCCATCCAGGCCGTCCTCTCTCTGTATGCCAGTGGTCGTACCACAGgtgagcacattcgacactgaactaaaaggctgtgaggatgaattttaattttgacattcac-atgtagatgagatttagttctgcaatcttcaattgtcat

upper sequence: GRMZM2G152328_T02 (Zea mays), 5'ss of exon 2
lower sequence: EDO98923 (Chlamydomonas reinhardtii), 5'ss of exon 5

GAGAAGATGACCCAGATCATGTTCGAGACCTTCAACACCCCGGCTATGTACGTCGCCATCCAGGCCGT----GCTCTCTCTGTATGCCAGTGGCCGTACCACAGgtgagc-tgattccgttctctgcttaacaatttccaaatccgatttgctcctgcagtccgttatctctaatatctgtggcttcccctctctcag
               |||||||||||||||||||||   ||||| |||||||| || |||||||        |      | |      |  |||||   ||  |  |  |  |    |   |   ||   ||| |     |  || |  | |  | || ||| |                                  
---------------ATCATGTTCGAGACCTTCAACGTGCCGGCCATGTACGTGGCTATCCAGgtgagagaggtcgagacagcggagtaacggccgcggcatcgcggcacgcggcagcagcccgagccggacagtaaggcaggccca--tacaacagcggtcggc---------------------------------

upper sequence: GRMZM2G152328_T02 (Zea mays), 5'ss of exon 2
lower sequence: PP1S372_48V6.1 (Physcomitrella patens), 5'ss of exon 2

GAGAAGATGACCCAGATCATGTTCGAGACCTTCAACACCCCGGCTATGTACGTCGCCATCCAGGCCGTGCTCTCTCTGTATGCCAGTGGCCGTACCACAGgtgagctgattccgttctctgcttaacaatttccaaatccgatttgctcctgcagtccg---ttatctctaatatctgtggcttcccctct--ctcag
||||||||||| ||||||||||||||||| ||||||   ||||| |||||||| || |||||||| ||||| || ||||| || || || || || || ||||||  |     |     ||                   | |  | |   |  ||  |   | ||    || |  ||||||    | |      |||
GAGAAGATGACGCAGATCATGTTCGAGACGTTCAACGTGCCGGCGATGTACGTGGCGATCCAGGCGGTGCTGTCGCTGTACGCGAGCGGGCGAACGACGGgtgagtggggagtgagtggtgagggggtggggatggtggtggtaggatgtggaggtgggaggtgattgagaacagatgtggcggtgcgtggaatgcag

upper sequence: GRMZM2G152328_T02 (Zea mays), 5'ss of exon 2
lower sequence: PP1S337_21V6.2 (Physcomitrella patens), 5'ss of exon 4

GAGAAGATGACCCAGATCATGTTCGAGACCTTCAACACCCCGGCTATGTACGTCGCCATCCAGGCCGTGCTCTCTCTGTATGCCAGTGGCCGTACCACAGgtgagctgattccgttctctgcttaacaatttccaaatccgatttgctcctgcagtccgtta---tctcta-atatctgtggcttcccctctctcag-------------------------------------------------------------
||||||||||| ||||||||||||||||| ||||||   ||||| |||||||| ||||| ||||| ||||| || || ||||||||||| || || || |||||| ||||          |       | | |   ||  |  ||| |   | |    ||     | | |  | |  || ||  |      |   |                                                              
GAGAAGATGACGCAGATCATGTTCGAGACGTTCAACGTGCCGGCGATGTACGTGGCCATTCAGGCAGTGCTGTCACTATATGCCAGTGGACGAACGACCGgtgag-tgatgggagaaggggtgaggtgaatgcagcatgtgcgttggttgcgaaagtggtggaggtgtgtggagaggtggggtgtttgacatgggaaggtttgtgggtcggggtaagaaactgagagcagttgtggtgatgaatgcaatgcaatgcag

upper sequence: GRMZM2G152328_T02 (Zea mays), 5'ss of exon 2
lower sequence: EFJ17401 (Selaginella moellendorffii), 5'ss of exon 2

GAGAAGATGACCCAGATCATGTTCGAGACCTTCAACACCCCGGCTATGTACGTCGCCATCCAGGCCGTGCTCTCTCTGTATGCCAGTGGCCGTACCACAGgt--gagctgattccgttctctgcttaacaatttccaaat--ccgatt--tgctcctgcagtccgttatctctaatatctgtg--gcttcccctctctcag-------------------------------------------------
|||||||||||||||||||||||||||||||||||   |||||| |||||||| || ||||| || || || || || || || ||||| || || || |||  |   |  ||   | |  |||||        | | ||    |||   || | ||    | ||||   |   |||    ||  |||||   |   |                                                    
GAGAAGATGACCCAGATCATGTTCGAGACCTTCAATGTCCCGGCCATGTACGTGGCGATCCAAGCAGTCCTTTCACTCTACGCGAGTGGACGCACTACCGgtatggagtttttttatcccttgcttgttctagacaagatggttgatgcgtgtttcttttcttcgttgcttgcgatagacatgatgcttcaagttggttctacttttgtttttccctctaacacgttgtatgatcgtggtttgtgatcag

upper sequence: GRMZM2G152328_T02 (Zea mays), 5'ss of exon 2
lower sequence: EFJ35077 (Selaginella moellendorffii), 5'ss of exon 2

GAGAAGATGACCCAGATCATGTTCGAGACCTTCAACACCCCGGCTATGTACGTCGCCATCCAGGCCGTGCTCTCTCTGTATGCCAGTGGCCGTACCACAGgt---gagctgattccgttctctgcttaacaatttccaaat--ccgatt--tgctcctgcagtccgttatctctaatatctgtg--gcttcccctctctcag--------------------------------------------------
|||||||||||||||||||||||||||||||||||   |||||| |||||||| || ||||| || || || || || || || ||||| || || || |||   ||| |  ||   | || |||||        | | ||    |||   || | ||    | ||||   |   |||    ||  |||||   |   |                                                     
GAGAAGATGACCCAGATCATGTTCGAGACCTTCAATGTCCCGGCCATGTACGTGGCAATCCAAGCAGTCCTTTCACTCTACGCGAGTGGACGCACTACCGgtatggagttttttttttcctttgcttgttctagacaagatggttgatgcgtgtttcttttcttcgttgcttgcgatagacatgatgcttcaagttggttctacttttttttcttctctctaacacgttgtatgatcgtggtttgtgatcag

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|6918758|gb|AW400288.1|AW400288

EST:     CGTCGCCATCCAGGCCGTGCTCTCTCTGTATGCCAGTGGCCGTACCACAG                         GTATCGTGCTCGACTCGGGAGATGGTGTGAGCCACACCGTCCCCATCTACG
genomic: CGTCGCCATCCAGGCCGTGCTCTCTCTGTATGCCAGTGGCCGTACCACAGgtgagctgat ... cctctctcagGTATCGTGCTCGACTCGGGAGATGGTGTGAGCCACACCGTCCCCATCTACG

EST: gi|7145305|gb|AW506786.1|AW506786

EST:     CGTCGCCATCCAGGCCGTGCTCTCTCTGTATGCCAGTGGCCGTACCACAG                         GTATCGTGCTCGACTCGGGAGATGGTGTGAGCCACACCGTCCCCATCTACG
genomic: CGTCGCCATCCAGGCCGTGCTCTCTCTGTATGCCAGTGGCCGTACCACAGgtgagctgat ... cctctctcagGTATCGTGCTCGACTCGGGAGATGGTGTGAGCCACACCGTCCCCATCTACG

EST: gi|6095303|gb|AW119970.1|AW119970

EST:     GGCCGTACCACAG                         GTATCGTGCTCGACTCGGGAGATGGTGTGAGCCACACCGTCCCCATCTACG
genomic: GGCCGTACCACAGgtgagctgat ... cctctctcagGTATCGTGCTCGACTCGGGAGATGGTGTGAGCCACACCGTCCCCATCTACG

EST: gi|211520844|gb|FL034051.1|FL034051

EST:     CGTCGCCATCCAGGCCGTGCTCTCTCTGTATGCCAGTGGCCGTACCACAG                         GTATCGTGCTCGACTCGGGAGATGGTGTGAGCCACA-CGTCCCCATCTACG
genomic: CGTCGCCATCCAGGCCGTGCTCTCTCTGTATGCCAGTGGCCGTACCACAGgtgagctgat ... cctctctcagGTATCGTGCTCGACTCGGGAGATGGTGTGAGCCACACCGTCCCCATCTACG

EST: gi|78180780|gb|DV551153.1|DV551153

EST:     CGTCGCCATCCAGGCCGTGCTCTCTCTGTATGCCAGTGGCCGTACCACAG                         GTATCGTGCTCGACTCGGGAGATGGTGTGAGCCACACCGTCCCCATCTACG
genomic: CGTCGCCATCCAGGCCGTGCTCTCTCTGTATGCCAGTGGCCGTACCACAGgtgagctgat ... cctctctcagGTATCGTGCTCGACTCGGGAGATGGTGTGAGCCACACCGTCCCCATCTACG

EST: gi|67017533|gb|CO446282.1|CO446282

EST:     CGTCGCCATCCAGGCCGTGCTCTCTCTGTATGCCAGTGGCCGTACCACAG                         GTATCGTGCTCGACTCGGGAGATGGTGTGAGCCACACCGTCCCCATCTACG
genomic: CGTCGCCATCCAGGCCGTGCTCTCTCTGTATGCCAGTGGCCGTACCACAGgtgagctgat ... cctctctcagGTATCGTGCTCGACTCGGGAGATGGTGTGAGCCACACCGTCCCCATCTACG

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: 49 (upstream exon), 49 (downstream exon)
Score: 216

GAGAAGATGACCCAGATCATGTTCGAGACCTTCAACACCCCGGCTATGTACGTCGCCATCCAGGCCGTGCTCTCTCTGTATGCCAGTGGCCGTACCACAGgtgagctgat ... cctctctcagGTATCGTGCTCGACTCGGGAGATGGTGTGAGCCACACCGTCCCCATCTACGAGGGATACGCCCTCCCCCACGCCATCCTTCGTCTTGACCTGGCCGGTCG

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 38

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