ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

TGGCTGCTCATCTTACAGGAATACACAGTGCCATCAAGATGCTCAATAGCAGGGTCCGTGTTATCCATCAGTATCTTGTTGCCATGCAAAAAGgtccgtacatatatgaagtgctacatttttttctctttactgaaataatgctatattgtgctagcttttcaaacatgctttcattcatgattcatctttaaacctaaacctttagaactctaatttcccaaacttgttaatggccctgttggatttttgccttgagaaaactgcagtgcaaagccttttgttcactgcag

Basic information

species	Zea mays
transcript	GRMZM2G028089_T01
intron #	6
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G028089_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os08g39070.1 (Oryza sativa), 5'ss of exon 6

TGGCTGCTCATCTTACAGGAATACACAGTGCCATCAAGATGCTCAATAGCAGGGTCCGTGTTATCCATCAGTATCTTGTTGCCATGCAAAAAGgtccgtacatatatgaagtgctacatttttttctctttactgaaataatgctatattgtgctagcttttcaaacatgctttcattcatgatt--catctttaaacctaaacctttag-aactctaatttcccaaacttgttaatggccctgttggatttttgccttgagaaaactgcagtgcaaagccttttgttcactgcag
||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||| ||||||| ||||||      || | |    || | | | ||   | ||      |||||   ||    |  | | |   || ||| ||  ||  |   ||| ||  || || | |    |||    ||  |||| ||| | ||   ||   | | ||                                                          
TGGCTGCTCATCTGACAGGAATACACAGTGCCATCAAGATGCTCAATAGCAGGGTCCGTGTTATCCATCAATATCTTGTTTCCATGCAGAAAGgt------attttt----tgttgc-tgttgagccctc----aaaatatgtctgctattcgat-gtgcttgaaatatagttcaaaatatgtttgccacctgttacttcaaataggtatcaactgtaaatccctttacc-atcactgcag-------------------------------------------------------

upper sequence: GRMZM2G028089_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA04G12890.1 (Glycine max), 5'ss of exon 6

TGGCTGCTCATCTTACAGGAATACACAGTGCCATCAAGATGCTCAATAGCAGGGTCCGTGTTATCCATCAGTATCTTGTTGCCATGCAAAAAGgtccgtacatatatgaagtgctacatttttttctctttactgaaataatgctatattgtgctagcttttcaaacatgctttcattcatgattcatctttaaacctaaacctttagaactctaatttcccaaacttgttaatggccctgttggatttttgccttgagaaaactgcagtgcaaagccttttgttcactgcag
|||||||||| ||||| |||||||||||||||||||| |||||  |||||||  |    ||  | ||||| |||||| |||| ||||||||||||  |    |||      ||| | | |    | |    | | ||||| |  |   |  |   |   || |||   |  |   |   || |||| | || | |                                                                                                  
TGGCTGCTCACCTTACTGGAATACACAGTGCCATCAAAATGCTTCATAGCAGAATAAAGGTGCTACATCACTATCTTCTTGCAATGCAAAAAGgtatgaggttatcctttctgcaaaaatagcatttgaa-aataaaatattatttgttattagaaatcttccaagtcttataaaaaatattattc-ttttgata--------------------------------------------------------------------------------------------------

upper sequence: GRMZM2G028089_T01 (Zea mays), 5'ss of exon 6
lower sequence: AT5G56280.1 (Arabidopsis thaliana), 5'ss of exon 6

TGGCTGCTCATCTTACAGGAATACACAGTGCCATCAAGATGCTCAATAGCAGGGTCCGTGTTATCCATCAGTATCTTGTTGCCATGCAAAAAGgtccgtacatatatgaagtgctacatttttttctctttactgaaataatgctatattgtgctagcttttcaaacatgctttcattcatgattcatctttaaacctaaacctttagaactctaatttcccaaacttgttaatggccctgttggatttttgccttgagaaaactgcagtgcaaagccttttgttcactgcag
|||||||||||||||| || ||||| ||||||||||||||||| ||||||||  || | ||  |  | ||  |||||| ||| ||||| ||||||   | |     ||   |    ||  ||    |  |||      |  |   || || | | ||      |  |  |||     |  | |    | | |||   |||   ||||    |||     | ||    |||   | |                                                         
TGGCTGCTCATCTTACTGGTATACATAGTGCCATCAAGATGCTTAATAGCAGAATCAGAGTGCTTTACCAAAATCTTGCTGCAATGCAGAAAGgtatattc-----tgttctttcccaagttccgattcttatcaccgtggtttcatgtt-taccagtccaggattctagctgaagatagtcaaagttgtgtaagtgtaataattta----tctgccaactcatttatgtgtgtag---------------------------------------------------------

upper sequence: GRMZM2G028089_T01 (Zea mays), 5'ss of exon 6
lower sequence: AT4G26430.1 (Arabidopsis thaliana), 5'ss of exon 6

TGGCTGCTCATCTTACAGGAATACACAGTGCCATCAAGATGCTCAATAGCAGGGTCCGTGTTATCCATCAGTATCTTGTTGCCATGCAAAAAGgtccgtacatatatgaagtgctacatttttttctctttactgaaataatgctatattgtgctagcttttcaaacatg-ctttcattcatgattcatctttaaacctaaacctttagaactctaatttcccaaact-tgttaatggccctgttggatttttgccttgagaaaactgcagtgcaaa-gccttttgtt-cactgcag----
|||||||||||||||| |||||||| ||||||||||||||||| ||||||||  || | ||  |  | ||| || |||| || ||||| ||||||   | | |     |    | ||  |   | |   ||             | | ||   | |||||||   || || |  |   || |     || | ||    |   |||   |      ||      |||   |||||   |        ||||||   |   |||  | ||  || | || | ||| |||    |||||     
TGGCTGCTCATCTTACTGGAATACATAGTGCCATCAAGATGCTTAATAGCAGAATCAGAGTGCTATACCAGCATATTGTCGCTATGCAGAAAGgtatattcttgctcaagtccccactctcggtccctctt----------caatttgttaatcaagcttttgtgacctgtcccttgatcttagaatatttctatgtgttttcctacggggaagaaagaattaaaagggtgttagaagat------gattttgagc--aagagtaatgtggtactaatgacttatgtgattctgcatctag

upper sequence: GRMZM2G028089_T01 (Zea mays), 5'ss of exon 6
lower sequence: Vv19s0015g01950.t01 (Vitis vinifera), 5'ss of exon 6

TGGCTGCTCATCTTACAGGAATACACAGTGCCATCAAGATGCTCAATAGCAGGGTCCGTGTTATCCATCAGTATCTTGTTGCCATGCAAAAAGgtccgtacatatatgaagtgctacatttttttctctttactgaaataatgctatattgtgctagcttttcaaacatgctttcattcatgattcatctttaaacctaaacctttagaactctaatttcccaaacttgttaatggccctgttggatttttgccttgagaaaactgcagtgcaaagccttttgttcactgcag
||||||| || || || || ||||| ||||||||||||||||| ||||||||  |||||||| | ||||| |||||  |||| ||||||||||||   |   | | |    |  |      |||    ||     || || ||  | |  |     | |||||    | |     |   |      |    |||                                                                                                   
TGGCTGCCCACCTCACGGGGATACATAGTGCCATCAAGATGCTAAATAGCAGAATCCGTGTTCTTCATCATTATCTGCTTGCTATGCAAAAAGgtgtatgtcttttttgtttatttagaaatttgaatttgttcaaagtagtggaagagaggataggattttctc-taagaaaaaacatagaggaaagaactaa---------------------------------------------------------------------------------------------------

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|211278074|gb|FL458563.1|FL458563

EST:     CAATAGCAGGGTCCGTGTTATCCATCAGTATCTTGTTSCCATSCAAAAAG                         GTGACATTCCAATGGACAATTCGCTGCTTAGGCAAGTCTCAAGCCTTGTAA
genomic: CAATAGCAGGGTCCGTGTTATCCATCAGTATCTTGTTGCCATGCAAAAAGgtccgtacat ... ttcactgcagGTGACATTCCAATGGACAATTCGCTGCTTAGGCAAGTCTCAAGCCTTGTAA

EST: gi|5343228|gb|AI795413.1|AI795413

EST:     CAATAGCAGGGTCCGTGTTATCCATCAGTATCTTGTTGCCATGCAAAAAG                         GTGACATTCCAATGGACAATTCGCTGCTTAGGCAAGTCTCAAGCCTTGTAA
genomic: CAATAGCAGGGTCCGTGTTATCCATCAGTATCTTGTTGCCATGCAAAAAGgtccgtacat ... ttcactgcagGTGACATTCCAATGGACAATTCGCTGCTTAGGCAAGTCTCAAGCCTTGTAA

EST: gi|74245516|gb|DT653430.1|DT653430

EST:     CAATAGCAGGGTCCGTGTTATCCATCAGTATCTTGTTGCCATGCAAAAAG                         GTGACATTCCNATGGACAATTCGCTGCTTA
genomic: CAATAGCAGGGTCCGTGTTATCCATCAGTATCTTGTTGCCATGCAAAAAGgtccgtacat ... ttcactgcagGTGACATTCCAATGGACAATTCGCTGCTTA

EST: gi|37383993|gb|CF629039.1|CF629039

EST:     CAATAGCAGGGTCCGTGTTATCCATCAGTATCTTGTTGCCATGCAAAAAG                         GTGACATTCCAATGGACAATTCGCTGCTTAGGCAAGTCTCAAGCCTTGTAA
genomic: CAATAGCAGGGTCCGTGTTATCCATCAGTATCTTGTTGCCATGCAAAAAGgtccgtacat ... ttcactgcagGTGACATTCCAATGGACAATTCGCTGCTTAGGCAAGTCTCAAGCCTTGTAA

EST: gi|37378561|gb|CF625975.1|CF625975

EST:     CAATAGCAGGGTCCGTGTTATCCATCAGTATCTTGTTGCCATGCAAAAAG                         GTGACATTCCAATGGACAATTCGCTGCTTAGGCAAGTCTCAAGCCTTGTAA
genomic: CAATAGCAGGGTCCGTGTTATCCATCAGTATCTTGTTGCCATGCAAAAAGgtccgtacat ... ttcactgcagGTGACATTCCAATGGACAATTCGCTGCTTAGGCAAGTCTCAAGCCTTGTAA

EST: gi|71428766|gb|DR809816.1|DR809816

EST:     CAATAGCAGGGTCCGTGTTATCCATCAGTATCTTGTTGCCATGCAAAAAG                         GTGACATTCCAATGGACAATTCGCTGCTTAGGCAAGTCTCAAGCCTTGTAA
genomic: CAATAGCAGGGTCCGTGTTATCCATCAGTATCTTGTTGCCATGCAAAAAGgtccgtacat ... ttcactgcagGTGACATTCCAATGGACAATTCGCTGCTTAGGCAAGTCTCAAGCCTTGTAA

EST: gi|78079913|gb|DV508325.1|DV508325

EST:     CAATAGCAGGGTCCGTGTTATCCATCAGTATCTTGTTGCCATGCAAAAAG                         GTGACATTCCAATGGACAATTCGCTGCTTAGGCAAGTCTCAAGCCTTGTAA
genomic: CAATAGCAGGGTCCGTGTTATCCATCAGTATCTTGTTGCCATGCAAAAAGgtccgtacat ... ttcactgcagGTGACATTCCAATGGACAATTCGCTGCTTAGGCAAGTCTCAAGCCTTGTAA

EST: gi|5847033|gb|AW000112.1|AW000112

EST:     CAATAGCAGGGTCCGTGTTATCCATCAGTATCTTGTTGCCATGCAAAAAG                         GTGACATTCCAATGGCCAATTCGCTGCTTAGGCAAGTCTCAAGCCTTGTAA
genomic: CAATAGCAGGGTCCGTGTTATCCATCAGTATCTTGTTGCCATGCAAAAAGgtccgtacat ... ttcactgcagGTGACATTCCAATGGACAATTCGCTGCTTAGGCAAGTCTCAAGCCTTGTAA

EST: gi|78104235|gb|DV522653.1|DV522653

EST:     CAATAGCAGGGTCCGTGTTATCCATCAGTATCTTGTTGCCATGCAAAAAG                         GTGACATTCCAATGGACAATTCGCTGCTTAGGCAAGTCTCAAGCCTTGTAA
genomic: CAATAGCAGGGTCCGTGTTATCCATCAGTATCTTGTTGCCATGCAAAAAGgtccgtacat ... ttcactgcagGTGACATTCCAATGGACAATTCGCTGCTTAGGCAAGTCTCAAGCCTTGTAA

EST: gi|5650012|gb|AI920372.1|AI920372

EST:     CAATAGCAGGGTCCGTGTTATCCATCAGTATCTTGTTGCCATGCAAAAAG                         GTGACATTCCAATGGACAATTCGCTGCTTAGGCAAGTCTCAAGCCTTGTAA
genomic: CAATAGCAGGGTCCGTGTTATCCATCAGTATCTTGTTGCCATGCAAAAAGgtccgtacat ... ttcactgcagGTGACATTCCAATGGACAATTCGCTGCTTAGGCAAGTCTCAAGCCTTGTAA

EST: gi|76925807|gb|DV170603.1|DV170603

EST:     AATAGCAGGGTCCGTGTTATCCATCAGTATCTTGTTTGC-ATGCAAAAAA                         GTGACATTCCCATGGACAATTCGCTGCTT
genomic: AATAGCAGGGTCCGTGTTATCCATCAGTATCTTGTT-GCCATGCAAAAAGgtccgtacat ... ttcactgcagGTGACATTCCAATGGACAATTCGCTGCTT

EST: gi|74245515|gb|DT653429.1|DT653429

EST:     CAATAGCAGGGTCCGTGTTATCCATCAGTATCTTGTTGCCATGCAAAAAG                         GTGACATTCCAATGGACAATTCGCTGCTTAGGCAAGTCTCAAGCCTTGTAA
genomic: CAATAGCAGGGTCCGTGTTATCCATCAGTATCTTGTTGCCATGCAAAAAGgtccgtacat ... ttcactgcagGTGACATTCCAATGGACAATTCGCTGCTTAGGCAAGTCTCAAGCCTTGTAA

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: 47 (upstream exon), 48 (downstream exon)
Score: 90

TGGCTGCTCATCTTACAGGAATACACAGTGCCATCAAGATGCTCAATAGCAGGGTCCGTGTTATCCATCAGTATCTTGTTGCCATGCAAAAAGgtccgtacat ... ttcactgcagGTGACATTCCAATGGACAATTCGCTGCTTAGGCAAGTCTCAAGCCTTGTAAGAAGGCTACCGGCTACGGAATCACAGAAATTCCAAGATGACTTTTTAAT

Block sizes: 47 (upstream exon), 46 (downstream exon)
Score: 39

Block sizes: 47 (upstream exon), 44 (downstream exon)
Score: 38