ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

ATAAGATTGTTGCTCCAGACACCAAGAACTCATTATCAGATCCATACCCTTTTAATCTCATGTTTCAAACTTCCATTGGACCATCAGGTTTGAGCCCAGGgtaagacaataacggctgaataaatttcagtatatttccactatgttcatccggcttaagtgtatctgcttccttggttttgcag

Basic information

species	Zea mays
transcript	GRMZM2G171688_T01
intron #	2
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G171688_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os04g32650.1 (Oryza sativa), 5'ss of exon 2

ATAAGATTGTTGCTCCAGACACCAAGAACTCATTATCAGATCCATACCCTTTTAATCTCATGTTTCAAACTTCCATTGGACCATCAGGTTTGAGCCCAGGgtaaga-caataacggctgaataaatttcagtatatttccactatgttcatccggcttaagtgtatctgcttccttggttttgcag
||   |||||||||||||||||||||||| | || ||||| |||||||| ||||| |||||||||||||||||||||||||||||||| ||||||||||||| ||  ||| ||| ||| ||||  |||     || |||   |||     || |  ||||   ||| |||||||| ||||||  ||
ATGGCATTGTTGCTCCAGACACCAAGAACCCGTTGTCAGACCCATACCCCTTTAACCTCATGTTTCAAACTTCCATTGGACCATCAGGCTTGAGCCCAGGgtgaggtcaagaacagctcaatattttt----gtacttcatttat-----tctgctttaaacttatgtgcttcctcggtttt-tag

upper sequence: GRMZM2G171688_T01 (Zea mays), 5'ss of exon 2
lower sequence: AT1G29880.1 (Arabidopsis thaliana), 5'ss of exon 2

ATAAGATTGTTGCTCCAGACACCAAGAACTCATTATCAGATCCATACCCTTTTAATCTCATGTTTCAAACTTCCATTGGACCATCAGGTTTGAGCCCAGGgtaagacaataacg-gctgaataaatttcagtatatttccactatgttcatccggcttaagtgtatctgcttccttggttttgcag
||  |||   |||||||||||| |||||  || | || ||||| ||||| |||||| | ||||||||||| |||||||| ||||| |||||||  || |||| ||    |  |  | |  |   ||||| |      |    |   |   |  |   | |   ||    | || || || || |||
ATGGGATCACTGCTCCAGACACGAAGAATCCACTCTCTGATCCTTACCCGTTTAATTTGATGTTTCAAACATCCATTGGCCCATCTGGTTTGATTCCTGGgtgagtatttttcatgttataatcatttctgagccactttctttcctgagtttgttatcaaattact--cctcttttgtgtttcag

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|211446350|gb|FL194324.1|FL194324

EST:     TTTAATCTCATGTTTCAAACTTCCATTGGACCATCAGGTTTGAGCCCAGG                         GTATATGAGGCCANAGACAGCTCAGGGTATATTTGTGAACTTC
genomic: TTTAATCTCATGTTTCAAACTTCCATTGGACCATCAGGTTTGAGCCCAGGgtaagacaat ... ggttttgcagGTATATGAGGCCAGAGACAGCTCAGGGTATATTTGTGAACTTC

EST: gi|148972573|gb|EE023537.2|EE023537

EST:     TTTAATCTCATGTTTCAAACTTCCATTGGACCATCAGGTTTGAGCCCAGG                         GTATATGAGGCCAGAGACAGCTCAGGGTATATTTGTGAACTTCAAAGACTT
genomic: TTTAATCTCATGTTTCAAACTTCCATTGGACCATCAGGTTTGAGCCCAGGgtaagacaat ... ggttttgcagGTATATGAGGCCAGAGACAGCTCAGGGTATATTTGTGAACTTCAAAGACTT

EST: gi|211446351|gb|FL194325.1|FL194325

EST:     TTTAATCTCATGTTTCAAACTTCCATTGGACCATCAGGCTTGAGCCCAGG                         GTATATGAGGCCAGAGACAGCTCAGGGTATATTTGTGAACTTCAAAGACTT
genomic: TTTAATCTCATGTTTCAAACTTCCATTGGACCATCAGGTTTGAGCCCAGGgtaagacaat ... ggttttgcagGTATATGAGGCCAGAGACAGCTCAGGGTATATTTGTGAACTTCAAAGACTT

EST: gi|13126604|gb|BG317174.1|BG317174

EST:     TTTAATCTCATGTTTCAAACTTCCATTGGACCATCAGGTTTGAGCCCAGG                         GTATATGAGGCCAGAGACAGCTCAGGGTATATTTGTGAACTTCAAAGACTT
genomic: TTTAATCTCATGTTTCAAACTTCCATTGGACCATCAGGTTTGAGCCCAGGgtaagacaat ... ggttttgcagGTATATGAGGCCAGAGACAGCTCAGGGTATATTTGTGAACTTCAAAGACTT

EST: gi|60342069|gb|DN209042.1|DN209042

EST:     TTTAATCTCATGTTTCAAACTTCCATTGGACCATCAGGTTTGAGCCCAGG                         GTATATGAGGCCAGAGACAGCTCAGGGTATATTTGTGAACTTCAAAGACTT
genomic: TTTAATCTCATGTTTCAAACTTCCATTGGACCATCAGGTTTGAGCCCAGGgtaagacaat ... ggttttgcagGTATATGAGGCCAGAGACAGCTCAGGGTATATTTGTGAACTTCAAAGACTT

EST: gi|211446352|gb|FL194326.1|FL194326

EST:     TTTAATCTCATGTTTCAAACTTCCATTGGACCATCAGGTTTGAGCCCAGG                         GTATATGAGGCCAGAGACAGCTCAGGGTATATTTGTGAACTTCAAAGACTT
genomic: TTTAATCTCATGTTTCAAACTTCCATTGGACCATCAGGTTTGAGCCCAGGgtaagacaat ... ggttttgcagGTATATGAGGCCAGAGACAGCTCAGGGTATATTTGTGAACTTCAAAGACTT

EST: gi|47961805|gb|CN844514.1|CN844514

EST:     TTAATCTCATGTTTCAAACTTCCATTGGGACCATCAGGTTTGAGCCCAGG                         GTATATGAGGCCAGAGACAGCTCAGGGTATATTTGTGAACTTCAAAGACTT
genomic: TTAATCTCATGTTTCAAACTTCCATTGG-ACCATCAGGTTTGAGCCCAGGgtaagacaat ... ggttttgcagGTATATGAGGCCAGAGACAGCTCAGGGTATATTTGTGAACTTCAAAGACTT

EST: gi|31354132|gb|CD438489.1|CD438489

EST:     TTTAATCTCATGTTTCAAACTTCCATCGGACCATCAGGTTTGAGCCCAGG                         GTATATGAGGCCAGAGACAGCTCAGGGTATATTTGTGAACTTCAAAGACTT
genomic: TTTAATCTCATGTTTCAAACTTCCATTGGACCATCAGGTTTGAGCCCAGGgtaagacaat ... ggttttgcagGTATATGAGGCCAGAGACAGCTCAGGGTATATTTGTGAACTTCAAAGACTT

EST: gi|211446355|gb|FL194329.1|FL194329

EST:     TTTAATCTCATGTTTCAAACTTCCATTGGACCATCAGGCTTGAGCCCAGG                         GTATATGAGGCCAGAGACAGCTCAGGGTATATTTGTGAACTTCAAAGACTT
genomic: TTTAATCTCATGTTTCAAACTTCCATTGGACCATCAGGTTTGAGCCCAGGgtaagacaat ... ggttttgcagGTATATGAGGCCAGAGACAGCTCAGGGTATATTTGTGAACTTCAAAGACTT

EST: gi|211446353|gb|FL194327.1|FL194327

EST:     TTTAATCTCATGTTTCAAACTTCCATTGGACCATCAGGCTTGAGCCCAGG                         GTATATGAGGCCAGAGACAGCTCAGGGTATATTTGTGAACTTCAAAGACTT
genomic: TTTAATCTCATGTTTCAAACTTCCATTGGACCATCAGGTTTGAGCCCAGGgtaagacaat ... ggttttgcagGTATATGAGGCCAGAGACAGCTCAGGGTATATTTGTGAACTTCAAAGACTT

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: 289

ATAAGATTGTTGCTCCAGACACCAAGAACTCATTATCAGATCCATACCCTTTTAATCTCATGTTTCAAACTTCCATTGGACCATCAGGTTTGAGCCCAGGgtaagacaat ... ggttttgcagGTATATGAGGCCAGAGACAGCTCAGGGTATATTTGTGAACTTCAAAGACTTGTATTACTACAATGGCAATAAGCTGCCATTCGCTGCAGCCCAAATTGGT

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 165

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 134