ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

CCATCTTGATCTTCATGCTGTGTTATGGCTAGAAACTTATCTCCTGAAGTGGCCAAAGACATTCATTGTTGTATCACACGCAAGGGAGTTTTTGAATACGgtatgaacacccaatatcatttcataggagctaattggacaaaatttgcactagcacatttttcttttcttgtgtggatttgaagtttatagtggatatttgacaacctgaactttttag

Basic information

species	Zea mays
transcript	GRMZM2G013890_T01
intron #	7
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G013890_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os02g58020.2 (Oryza sativa), 5'ss of exon 7

CCATCTTGATCTTCATGCTGTGTTATGGCTAGAAACTTATCTCCTGAAGTGGCCAAAGACATTCATTGTTGTATCACACGCAAGGGAGTTTTTGAATACGgtatg------aacacccaatatcatttcataggagc-taattggacaaaatttgcactagcacatttttcttttcttgtgtggatttgaagtttatagtggatatttgacaacctgaactttttag-----------------------
 ||||||||||| ||||||||||||||| ||||||| ||||||||||| ||||||||||||||||||||||||||||| || ||||||||| | |||||||||||       |     |  ||||| |||||  | | | |  |  | || ||||    |||    ||   |  | |   ||  ||||| | | |  | |   |   |    |  | ||    |||                        
TCATCTTGATCTCCATGCTGTGTTATGGTTAGAAACATATCTCCTGAAATGGCCAAAGACATTCATTGTTGTATCACATGCTAGGGAGTTTCTTAATACGgtatgcagtatgatgattatgatcatgtcatattatcatgaaggagctaattttgacagagcgtccttaattcatatgtagtatatttgca-tgtgcatttttttccttgtcatgtaaatcacttaatgctgatagcaataaattcttag

upper sequence: GRMZM2G013890_T01 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA20G16170.1 (Glycine max), 5'ss of exon 6

CCATCTTGATCTTCATGCTGTGTTATGGCTAGAAACTTATCTCCTGAAGTGGCCAAAGACATTCATTGTTGTATCACACGCAAGGGAGTTTTTGAATACGgtatgaacacccaatatcatttcataggagctaattggacaaaatttgcactagcacatttttcttttcttgtgtggatttgaagtttatagtggatatttgacaacctgaactttttag
 |||||||||||||||||||| |||||||| ||| ||||  |  | || |||||||| ||||| |||||||| || || || || || ||||| || ||||||   |||       | || | |    |  | ||| |       ||    | |   | |   ||||   |   ||  ||   ||  |||  |    | |||  |||   |  |    ||
TCATCTTGATCTTCATGCTGTCTTATGGCTTGAATCTTACTTGGTTAAATGGCCAAAAACATTTATTGTTGTTTCTCATGCTAGAGAATTTTTAAACACGgta---acatatcggcttatctta----atttgatttggtg----ttttgttggttaaatg--ctttctctaaatgtgttcccagcatatctttttaacttgttaactgca--tgcccag

upper sequence: GRMZM2G013890_T01 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA13G10530.1 (Glycine max), 5'ss of exon 6

CCATCTTGATCTTCATGCTGTGTTATGGCTAGAAACTTATCTCCTGAAGTGGCCAAAGACATTCATTGTTGTATCACACGCAAGGGAGTTTTTGAATACGgtatgaacacccaatatcatttcataggagctaattggacaaaat-ttgcactagcacatttttcttttcttgtgtggatttgaagtttatagtggatatttgacaacctgaactttttag
 |||||||||||||||||||| |||||||| ||| | ||  |  | || |||||||| ||||| || ||||| || || || || || ||||| || ||||||     ||   |||||   | ||      ||||| ||     | ||    | |   | |  | | |     ||||         | | |  |   |  || ||  | ||  |       
TCATCTTGATCTTCATGCTGTCTTATGGCTTGAATCGTACTTGGTTAAATGGCCAAAAACATTTATCGTTGTTTCTCATGCTAGAGAATTTTTAAACACGgta-----ac---atatcggcttatc----ttaatttgatctggtgttttgttggttaagtgctttctcaaaatgtgttcccagcatattttttaacttgttaactgcatgcccag-----

upper sequence: GRMZM2G013890_T01 (Zea mays), 5'ss of exon 7
lower sequence: AT1G64550.1 (Arabidopsis thaliana), 5'ss of exon 7

CCATCTTGATCTTCATGCTGTGTTATGGCTAGAAACTTATCTCCTGAAGTGGCCAAAGACATTCATTGTTGTATCACACGCAAGGGAGTTTTTGAATACGgtatgaacacccaatatcatttcataggagctaattggacaaaatttgcactagcacatttttcttttcttgtgtggatttgaagttta-tagtggatatttgacaacctgaactttttag
|||||||||||| |||||||| |||||| ||||||| |||||   |||||||||||| ||||| || || || || || || ||||| || ||||| ||||||        || | |  | ||    || ||  |||  ||    |||      || || | ||      |||||  |    | ||||  | |  |                         
CCATCTTGATCTCCATGCTGTCTTATGGTTAGAAACATATCTAACGAAGTGGCCAAAAACATTTATAGTCGTTTCCCATGCTAGGGAATTCTTGAACACGgta--------catttttttctctagtgatctccttg--cagttattgtttcccca-atatctccggatatgtgtaaaccatatgtttggttgcag-------------------------

upper sequence: GRMZM2G013890_T01 (Zea mays), 5'ss of exon 7
lower sequence: Vv02s0025g02160.t01 (Vitis vinifera), 5'ss of exon 7

CCATCTTGATCTTCATGCTGTGTTATGGCTAGAAACTTATCTCCTGAAGTGGCCAAAGACATTCATTGTTGTATCACACGCAAGGGAGTTTTTGAATACGgtatgaacacccaatatcatttcataggagctaattg--gacaaaatttgcactagc-acatttttcttttcttgtgtggatttgaagtttatagtgga-tatttgacaacctgaactttttag--
||||||||| ||||||||||| |||||||| || ||||| ||  |||| |||||||| ||| | || ||||| || || || || || || ||||| ||||||   | |  ||   ||  || |||    | | |||  || |||| |   | |    | ||| || || ||     | |     |  ||  | | | | | ||| |  | ||   ||||||    
CCATCTTGACCTTCATGCTGTTTTATGGCTGGAGACTTACCTGGTGAAATGGCCAAAAACAGTTATAGTTGTTTCTCATGCTAGAGAATTCTTGAACACGgta-acatattcaccttc-cttgatattt-ccagttgaagataaaagtattattgattagattgtttttctcaaaatttgccacaacattctttgagaagtttttcattaacttttctttttccag

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|33094472|gb|CF054466.1|CF054466

EST:     GGCCAAAGACATTCATTGTTGTATCACACGCAAGGGAGTTTTTGAATACG                         GTCGTCACCGATATCCTTCATCTGCATGGTAGAAAACTACATGCTTACAAA
genomic: GGCCAAAGACATTCATTGTTGTATCACACGCAAGGGAGTTTTTGAATACGgtatgaacac ... aactttttagGTTGTCACCGATATCCTTCATCTGCATGGTAGAAAACTACATGCTTACAAA

EST: gi|60343993|gb|DN210966.1|DN210966

EST:     GGCCAAAGACATTCATTGTTGTATCACACGCAAGGGAGTTTTTGAATACG                         GTTGTCACCGATATCCTTCATCTGCATGGTAGAAAACTACATGCTTACAAA
genomic: GGCCAAAGACATTCATTGTTGTATCACACGCAAGGGAGTTTTTGAATACGgtatgaacac ... aactttttagGTTGTCACCGATATCCTTCATCTGCATGGTAGAAAACTACATGCTTACAAA

EST: gi|211238345|gb|FL044423.1|FL044423

EST:     GGCCAAAGACATTCATTGTTGTATCACACGCAAGGGAGTTTTTGAATACG                         GTTGTCACCGATATCCTTCATCTGCATGGTAGAAAACTACATGCTTACAAA
genomic: GGCCAAAGACATTCATTGTTGTATCACACGCAAGGGAGTTTTTGAATACGgtatgaacac ... aactttttagGTTGTCACCGATATCCTTCATCTGCATGGTAGAAAACTACATGCTTACAAA

EST: gi|20301286|gb|BQ164229.1|BQ164229

EST:     GGCCAAAGACATTCATTGTTGTATCACACGCAAGGGAGTTTTTGAATACG                         GTTGTCACCGATATCCTTCATCTGCATGGTAGAAAAC
genomic: GGCCAAAGACATTCATTGTTGTATCACACGCAAGGGAGTTTTTGAATACGgtatgaacac ... aactttttagGTTGTCACCGATATCCTTCATCTGCATGGTAGAAAAC

EST: gi|60349362|gb|DN216335.1|DN216335

EST:     GGCCAAAGACATTCATTGTTGTATCACACGCAAGGGAGTTTTTGAATACG                         GTTGTCACCGATATCCTTCATCTGCATGGTAGAAAACTACATGCTTACAAA
genomic: GGCCAAAGACATTCATTGTTGTATCACACGCAAGGGAGTTTTTGAATACGgtatgaacac ... aactttttagGTTGTCACCGATATCCTTCATCTGCATGGTAGAAAACTACATGCTTACAAA

EST: gi|71307303|gb|DR789832.1|DR789832

EST:     GGCCAAAGACATTCATTGTTGTATCACACGCAAGGGAGTTTTTGAATACG                         GTTGTCACCGATATCCTTCATCTGCATGGTAGAAAACTACATGCTTACAAA
genomic: GGCCAAAGACATTCATTGTTGTATCACACGCAAGGGAGTTTTTGAATACGgtatgaacac ... aactttttagGTTGTCACCGATATCCTTCATCTGCATGGTAGAAAACTACATGCTTACAAA

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), 46 (downstream exon)
Score: 136

CCATCTTGATCTTCATGCTGTGTTATGGCTAGAAACTTATCTCCTGAAGTGGCCAAAGACATTCATTGTTGTATCACACGCAAGGGAGTTTTTGAATACGgtatgaacac ... aactttttagGTTGTCACCGATATCCTTCATCTGCATGGTAGAAAACTACATGCTTACAAAGGTGACTATGACACATTTGAGAGGACAAGGGAAGAGCACCTTAAGAATC

Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 139

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 128