ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GGTTCTGTGTATGTCTGCAATCTACCTCCTGGAACTGATGAAAATATGTTGGCTGAATATTTTGGCACCATAGGCTTGCTAAAGGTATGGGTCTTACCAGgtaacatttttggccactaccaaaaattttaagattgttcatacattttaaattccatttaaagaacacttagcctcgtctctgttgtaaaattgcaacag

Basic information

species	Zea mays
transcript	AC233865.1_FGT006
intron #	2
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: AC233865.1_FGT006 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os07g19560.1 (Oryza sativa), 5'ss of exon 2

----------------GGTTCTGTGTATGTCTGCAATCTACCTCCTGGAACTGATGAAAATATGTTGGCTGAATATTTTGGCACCATAGGCTTGCTAAAGGTATGGG-TCTTACCAGgtaacattttt--ggccactaccaaaaattttaagattgttcatacattttaaattccatttaaagaacacttagcctcgtctctgttgtaaaattgcaacag
                |||||||| ||||| |||||||| ||||||||||| ||||| |  ||| ||||||||||||||||||||||||| |||||||||||||||| |||| |||||||||||||||   |||||| | |||    | |||||| || |  |  ||     | || |      | | |||| |   | |||||| |  |  | ||| ||
AAGAGGCCCCCCAAATGGTTCTGTTTATGTATGCAATCTGCCTCCTGGAACCGATGAGACCATGCTGGCTGAATATTTTGGCACCATAGGGTTGCTAAAGgtatggggtcttcccaggtaacatttttaaagccacttcaaaattactgaagattctttaagccctt---gcttcagtgttgtgataattagtcat-tttctgttctcgatct-caatag

upper sequence: AC233865.1_FGT006 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os07g19560.2 (Oryza sativa), 5'ss of exon 2

GGTTCTGTGTATGTCTGCAATCTACCTCCTGGAACTGATGAAAATATGTTGGCTGAATATTTTGGCACCATAGGCTTGCTAAAGGTATGGG-TCTTACCAGgtaacatttttg--gccactaccaaaaattttaagattgttcatacattttaaattccatttaaagaacacttagcctcgtctctgttgtaaaattgcaacag
 ||||||| ||||| |||||||| ||||||||||| ||||| |  ||| ||||||||||||||||||||||||| |||||||||||||||| |||| |||||||||||||||   |||||| | |||    | |||||| || |  |  ||     | || |      | | |||| |   | |||||| |  |  | ||| ||
-GTTCTGTTTATGTATGCAATCTGCCTCCTGGAACCGATGAGACCATGCTGGCTGAATATTTTGGCACCATAGGGTTGCTAAAGGTATGGGGTCTTCCCAGgtaacatttttaaagccacttcaaaattactgaagattctttaagccctt---gcttcagtgttgtgataattagtcat-tttctgttctcgatct-caatag

upper sequence: AC233865.1_FGT006 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os09g12800.1 (Oryza sativa), 5'ss of exon 2

----------------GGTTCTGTGTATGTCTGCAATCTACCTCCTGGAACTGATGAAAATATGTTGGCTGAATATTTTGGCACCATAGGCTTGCTAAAGGTATGG------GTCTTACCAGgtaacatttttggccactaccaaaaattttaagattgttcatacattttaaattccatttaaagaacacttagcctcgtctctgttgtaaaattgcaacag
                || ||||| ||||| |||||||| ||||||||||| ||||| |  ||| |||| || ||||||||||||||||| ||||| |||||||||      ||||| ||||| ||||||||||    ||       |||  |||||| ||||  | |||     | |||||  |    | |||| |   | ||||||||  |  | ||||||
AAGAGGCCCCCCAAATGGCTCTGTTTATGTGTGCAATCTGCCTCCTGGAACCGATGAGACCATGCTGGCCGATTATTTTGGCACCATAGGGTTGCTGAAGgtatggatgggggtcttcccaggcaacatttttg-tagctg------attaaaagattcttcaagcctttgtcgcttcattttcatggtaattagtcat-tttctgttgttgatct-caacag

upper sequence: AC233865.1_FGT006 (Zea mays), 5'ss of exon 2
lower sequence: AT1G50300.1 (Arabidopsis thaliana), 5'ss of exon 2

----------------GGTTCTGTGTATGTCTGCAATCTACCTCCTGGAACTGATGAAAATATGTTGGCTGAATATTTTGGCACCATAGGCTTGCTAAAGGTATGGGTCTTACCAGgtaacatttttggccactaccaaaaattttaagattgttcatacattttaaattccatttaaagaacacttagcctcgtctctgttgtaaaattgcaacag
                || || || || || |  ||||| ||    |||||||| || |||||||||||||| |||||||| ||||| || ||||| |||||||||   |  |||||||  | || | ||   |        |||| |  |  ||   |  ||||| |   || |  |    |   |  | |    | | || || | |      ||
TGGATATCCTACTAATGGATCAGTCTACGTTTCAAATCTCCCCTTAGGAACTGACGAGAATATGTTGGCTGACTATTTTGGGACCATTGGGTTGCTTAAGgtatggtattggccaggtactaattgttgctttt-------gttttgacgtcattgcaatcttttataggtcactagattttcgagtttcttacatttttttctacattgcttttag

upper sequence: AC233865.1_FGT006 (Zea mays), 5'ss of exon 2
lower sequence: Vv01s0010g01410.t01 (Vitis vinifera), 5'ss of exon 1

----------------GGTTCTGTGTATGTCTGCAATCTACCTCCTGGAACTGATGAAAATATGTTGGCTGAATATTTTGGCACCATAGGCTTGCTAAAGGTA-TGGGTCTTACCAGgtaacatttttggccac-taccaaaaat-tttaagattgttcatacattttaaattccatttaaa--gaacacttagcctcgtctctgttgtaaaattgcaacag-------------
                || ||||| ||||| || ||  | |||| |||||||||||||| ||||||||||||||||||||||||||| || ||| |||||||| |   ||| ||  | ||  ||||       | ||       | ||| | |    |  |   || ||||      | |     ||  || | |||  |||    | |    |  ||                 
AGGAGCCCCTTCAAATGGCTCTGTCTATGTTTGTAACTTGCCTCATGGAACTGATGAAACTATGTTGGCTGAATATTTTGGCACCATTGGGTTGATAAAGgtagttaatctgactggctattatttgaaattccatattgtgcttgttttacaagccttttgttttgtaaaacttgataagttcaaatgctcatccttttcttccattttctttctcattcacgttcctttgtag

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|211325885|gb|FL059678.1|FL059678

EST:     TGAATATTTTGGCACCATA-GCTTGCCTATAAAGGTATGGGTCTTACCAG                         AAGGACAAAAGGACTGGGCGTCCAAAAATTTGGATATACAGGGACAAAGTT
genomic: TGAATATTTTGGCACCATAGGCTTG-C--TAAAGGTATGGGTCTTACCAGgtaacatttt ... attgcaacagAAGGACAAAAGGACTGGGCGTCCAAAAATTTGGATATACAGGGACAAAGTT

EST: gi|211328059|gb|FL059693.1|FL059693

EST:     TGAATATTTTGGCACCATAG-CT-GCGTAAAAAGTTATGGNTCTTACCAN                         AANGACAAAANGACTGGGCGTCCAAAAATTTGGATATACAGGGACAAAGTT
genomic: TGAATATTTTGGCACCATAGGCTTGC-TAAAG-GT-ATGGGTCTTACCAGgtaacatttt ... attgcaacagAAGGACAAAAGGACTGGGCGTCCAAAAATTTGGATATACAGGGACAAAGTT

EST: gi|211328057|gb|FL059691.1|FL059691

EST:     CTGAATATTTTGGCACCATAGTGCTTNNNNNNNGGTATGGGTCTTACCAN                         AAGGACAAAAGGACTGGGGCGTCCAAAAATTTGGATATACAGGGACAAAGT
genomic: CTGAATATTTTGGCACCATAG-GCTT-GCTAAAGGTATGGGTCTTACCAGgtaacatttt ... attgcaacagAAGGACAAAAGGACT-GGGCGTCCAAAAATTTGGATATACAGGGACAAAGT

EST: gi|211325889|gb|FL059682.1|FL059682

EST:     GCTGAATATTTTGGCACCATAGGCTTGCCTAAAGGTATGGGTCTTACCAG                         AAGGACAAAAGGACTGGGCGTCCAAAAATTTGGATATACAGGGACAAAGTT
genomic: GCTGAATATTTTGGCACCATAGGCTTGC-TAAAGGTATGGGTCTTACCAGgtaacatttt ... attgcaacagAAGGACAAAAGGACTGGGCGTCCAAAAATTTGGATATACAGGGACAAAGTT

EST: gi|211325891|gb|FL059684.1|FL059684

EST:     CTGAATATTTTGGCACCATAGTGTCCTA-TAAAGGTATGNNTCTTACCAG                         AAGGACAAAAGGACTGGGCGTCCAAAAATTTGGATATACAGGGACAAAGTT
genomic: CTGAATATTTTGGCACCATAG-G-CTTGCTAAAGGTATGGGTCTTACCAGgtaacatttt ... attgcaacagAAGGACAAAAGGACTGGGCGTCCAAAAATTTGGATATACAGGGACAAAGTT

EST: gi|211325887|gb|FL059680.1|FL059680

EST:     TAAAAAGGTATGGGNNCTTACCANN                         AANGACAAAAAGGACTGGGCGTCCAAAAATTTGGATATACAGGGACAAAG
genomic: TAAA--GGTATGGGT-CTTACCAG-gtaacatttt ... attgcaacagAAGGACAAAA-GGACTGGGCGTCCAAAAATTTGGATATACAGGGACAAAG

EST: gi|211325887|gb|FL059680.1|FL059680

EST:     TAAAAAGGTATGGGNNCTTACCANN                         AANGACAAAAAGGACTGGGCGTCCAAAAATTTGGATATACAGGGACAAAG
genomic: TAAA--GGTATGGGT-CTTACCAG-gtaacatttt ... attgcaacagAAGGACAAAA-GGACTGGGCGTCCAAAAATTTGGATATACAGGGACAAAG

EST: gi|211044975|gb|FL152243.1|FL152243

EST:     ATATTTTGGCACCATAGTGGCTT-CAAAAAGGGGTATGGGGTCTTACCAG                         AAGGACAAAANGGACTGGGCGTCCAAAAATTTGGATATACAGGGACAAAGT
genomic: ATATTTTGGCACCATAG-G-CTTGCTAAA-GG--TATGGG-TCTTACCAGgtaacatttt ... attgcaacagAAGGACAAAA-GGACTGGGCGTCCAAAAATTTGGATATACAGGGACAAAGT

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: 46 (upstream exon), 47 (downstream exon)
Score: 72

GGTTCTGTGTATGTCTGCAATCTACCTCCTGGAACTGATGAAAATATGTTGGCTGAATATTTTGGCACCATAGGCTTGCTAAAGGTATGGGTCTTACCAGgtaacatttt ... attgcaacagAAGGACAAAAGGACTGGGCGTCCAAAAATTTGGATATACAGGGACAAAGTTACTAATGAACCAAAGGGTGATGCAACAGTCACCTATGAGGATCCACATG

Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 113

Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 98