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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCACTGGCAAGGCAGTCATGCTCGATGAGATTATCAACTATGTGCAGTCATTGCAACGACAAGTCGAGgtagtgttagtgcatctgtagctgaattgttttggaatatatgtggcatcttgttagtatatatccagtattctaatacagtttcgagcttgcag

Basic information

species Zea mays
transcript GRMZM2G385543_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G385543_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os03g51910.1 (Oryza sativa), 5'ss of exon 5
ATCACTGGCAAGGCAGTCATGCTCGATGAGATTATCAACTATGTGCAGTCATTGCAACGACAAGTCGAGgtagtgttagtgcatctgtagctgaattgttttggaatatatgtggcatcttgttagtatat-atccagtattctaatacagtttcgagcttgcag
|||||||| |||||||||||||| |||||||| ||||| ||||| |||||| | ||||| ||||| |||||| | |||| |     || | | | || |||         |  | ||    ||| | |||| |  | ||| ||||| ||| | | || |||||||
ATCACTGGTAAGGCAGTCATGCTTGATGAGATAATCAATTATGTACAGTCACTACAACGTCAAGTTGAGgtactattagggtg---gtggttcagttatttc--------ttggaca----gttggaatatcactctgtaatctaacacaatct-gaacttgcag

upper sequence: GRMZM2G385543_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA04G05090.1 (Glycine max), 5'ss of exon 6
ATCACTGGCAAGGCAGTCATGCTCGATGAGATTATCAACTATGTGCAGTCATTGCAACGACAAGTCGAGgtagtgttagtgcatctgtagctgaattgttttggaatatatgtggcatcttgttagtatatatccagtattctaatacagtttcgagcttgcag
|  || || || || || ||||| ||||||||||| ||||||||||| ||| |||||| ||| || |||||| || |  |   | | |||        | ||  || ||| |  |                                                 
AAAACGGGTAAAGCGGTAATGCTGGATGAGATTATAAACTATGTGCAATCACTGCAACAACAGGTTGAGgta-tgctgttatgtatttagtcttgcactcttacaa-ata-gcag-------------------------------------------------

upper sequence: GRMZM2G385543_T01 (Zea mays), 5'ss of exon 5
lower sequence: AT1G10120.1 (Arabidopsis thaliana), 5'ss of exon 4
ATCACTGGCAAGGCAGTCATGCTCGATGAGATTATCAACTATGTGCAGTCATTGCAACGACAAGTCGAGgtagtgttagtgcatctgtagctgaattgttttggaatatatgtggcatcttgtt----agtatatatccagtattctaatacagtttcgagcttg--cag
||||| || || || || ||||||||||| || ||||||||||| |||||||||||||  ||||| ||||||   |||   ||   |||     |   | ||| ||       |  |  ||| |    |  |  | | |  | ||  || || | ||  |  ||   |||
ATCACCGGAAAAGCGGTTATGCTCGATGAAATAATCAACTATGTTCAGTCATTGCAACAGCAAGTTGAGgtaagattatccca---gtaatgcgagattcttgaaactctcaagttagtttggtgtgaaagaggttttctttcttgaaaaactgcttttattttcttcag

upper sequence: GRMZM2G385543_T01 (Zea mays), 5'ss of exon 5
lower sequence: Vv18s0001g08600.t01 (Vitis vinifera), 5'ss of exon 4
ATCACTGGCAAGGCAGTCATGCTCGATGAGATTATCAACTATGTGCAGTCATTGCAACGACAAGTCGAGgta-gtgttagtgcatctgtagctgaattgttttggaatatatgtggcatcttgttag-tatatatccagtattctaatacagtttcgagcttgcag---
|| ||||| |||||||| ||||| |||||||||||||| ||||| |||||| |||||| ||| || |||||| |   | || || || ||    |   |  || |      ||||   |  | | || | |||||  |  |      ||   |    |      |    
ATTACTGGGAAGGCAGTAATGCTTGATGAGATTATCAATTATGTACAGTCACTGCAACAACAGGTTGAGgtatgccattgttcaactctaatataggggcattagtggtgttgtgctgttgtttaagatttatatttaagaaaaagttagcctcatcaatccttatatg

upper sequence: GRMZM2G385543_T01 (Zea mays), 5'ss of exon 5
lower sequence: Vv07s0151g00450.t01 (Vitis vinifera), 5'ss of exon 4
ATCACTGGCAAGGCAGTCATGCTCGATGAGATTATCAACTATGTGCAGTCATTGCAACGACAAGTCGAGgta-gtgttagtg-catctgtag------ctgaattgttttggaatatatgtggcatcttgttagtatatatccagtattctaatacagtttcgagcttgcag
|| ||||| || || || ||||| ||||||||||||||||||||||| ||| |||||||||| || |||||| | |||  ||  ||||| ||       |  ||   |||   ||  || |   |||   | |  |  |   | |    ||  || || |  ||   |    
ATTACTGGAAAAGCGGTAATGCTTGATGAGATTATCAACTATGTGCAATCACTGCAACGACAGGTTGAGgtatgcgtttctgatatctgaagaataagtttcatctctttattatgaatataaaatcacatgaagaattcctctgctgacttttaaagatctgaaacta---

upper sequence: GRMZM2G385543_T01 (Zea mays), 5'ss of exon 5
lower sequence: PP1S68_190V6.1 (Physcomitrella patens), 5'ss of exon 3
-------------------------------ATCACTGGCAAGGCAGTCATGCTCGATGAGATTATCAACTATGTGCAGTCATTGCAACGACAAGTCGAGgta-gtgt-tagtgcatctgtagctgaat-----tgttttggaatatatgt----ggca----tcttgttagtatatatccagtattctaatacagtttcgagcttgcag--------------------------
                                |||| ||||||||||||||||| || ||||| ||||||||||| || ||  | ||||||||||| || ||| || | |    ||| |  | |  | |     || | |   ||  ||||    ||||    ||||||||       |   | ||| || |  ||| | ||| ||| |                           
CCTGCAGGACCTCGTACCCGGCTGCCGCAAAGTCACCGGCAAGGCAGTCATGCTTGACGAGATCATCAACTATGTTCAATCCCTCCAACGACAAGTTGAAgtatgtctcttacccattttcaacgcactgctaatgctattccattcatgtcttaggcacccttcttgttatcgctagtgatgaattgtagtctagtattgag-ttgtatcgtacactttgttatcttttttacag

upper sequence: GRMZM2G385543_T01 (Zea mays), 5'ss of exon 5
lower sequence: PP1S69_95V6.1 (Physcomitrella patens), 5'ss of exon 2
-------------------------------ATCACTGGCAAGGCAGTCATGCTCGATGAGATTATCAACTATGTGCAGTCATTGCAACGACAAGTCGAGgtag-------------tgttagtgcatctgtagctgaat-tgttttggaatatatgtggca--tcttgttagtatatatccagtattctaatacagtttcgagcttgcag
                                |||||||||| ||||||||||||||||| || ||||| || || |||||  | ||||| ||||||||||||               |    |  ||    |  ||||  || |       || ||  | |  || | | ||  |||       | |   | |   |||     ||||||
CTTGCAGGACCTTGTTCCTGGCTGCCGCAAAGTCACTGGCAAAGCAGTCATGCTCGATGAAATCATCAATTACGTCCAGTCCCTCCAACGTCAAGTCGAGgtacatccctcattctccgccgttctatacacaattgaaggtggtgatagggatctgctgtaattcatatcaggttatgatgttaacttccacattttttttgtgttgcag

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|160481343|gb|EY254497.1|EY254497
EST:     TGCTCGATGAGATTATCAACTATGTGCAGTCATTGCAACGACAAGTCGAG                         TTCTTGTCAATGAAACTCGCAACTGTTAACCCCGAGCTTGGCTTTGACATT
genomic: TGCTCGATGAGATTATCAACTATGTGCAGTCATTGCAACGACAAGTCGAGgtagtgttag ... gagcttgcagTTCTTGTCAATGAAACTCGCAACTGTTAACCCCGAGCTTGGCTTTGACATT
EST: gi|160481403|gb|EY254527.1|EY254527
EST:     TGCTCGATGAGATTATCAACTATGTGCAGTCATTGCAACGACAAGTCGAG                         TTCTTGTCAATGAAACTCGCAACTGTTAACCCCGAGCTTGGCTTTGACATT
genomic: TGCTCGATGAGATTATCAACTATGTGCAGTCATTGCAACGACAAGTCGAGgtagtgttag ... gagcttgcagTTCTTGTCAATGAAACTCGCAACTGTTAACCCCGAGCTTGGCTTTGACATT
EST: gi|29167960|gb|CB411220.1|CB411220
EST:     TGCTCGATGAGATTATCAACTATGTGCAGTCATTGCAACGACAAGTCGAG                         TTCTTGTCAATGAAACTCGCAACTGTTAACCCCGAGCTTGGCTTTGACATT
genomic: TGCTCGATGAGATTATCAACTATGTGCAGTCATTGCAACGACAAGTCGAGgtagtgttag ... gagcttgcagTTCTTGTCAATGAAACTCGCAACTGTTAACCCCGAGCTTGGCTTTGACATT

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: 44 (upstream exon), 48 (downstream exon)
Score: 73

ATCACTGGCAAGGCAGTCATGCTCGATGAGATTATCAACTATGTGCAGTCATTGCAACGACAAGTCGAGgtagtgttag ... gagcttgcagTTCTTGTCAATGAAACTCGCAACTGTTAACCCCGAGCTTGGCTTTGACATTGAGCAGATCATATCCAAACAA


Block sizes: 45 (upstream exon), 20 (downstream exon)
Score: 4

ATCACTGGCAAGGCAGTCATGCTCGATGAGATTATCAACTATGTGCAGTCATTGCAACGACAAGTCGAGgtagtgttag ... gagcttgcagTTCTTGTCAATGAAACTCGCAACTGTTAACCCCGAGCTTGGCTTTGACATTGAGCAGATCATATCCAAACAA


Block sizes: 32 (upstream exon), 48 (downstream exon)
Score: 9

ATCACTGGCAAGGCAGTCATGCTCGATGAGATTATCAACTATGTGCAGTCATTGCAACGACAAGTCGAGgtagtgttag ... gagcttgcagTTCTTGTCAATGAAACTCGCAACTGTTAACCCCGAGCTTGGCTTTGACATTGAGCAGATCATATCCAAACAA


Block sizes: 30 (upstream exon), 44 (downstream exon)
Score: 5

ATCACTGGCAAGGCAGTCATGCTCGATGAGATTATCAACTATGTGCAGTCATTGCAACGACAAGTCGAGgtagtgttag ... gagcttgcagTTCTTGTCAATGAAACTCGCAACTGTTAACCCCGAGCTTGGCTTTGACATTGAGCAGATCATATCCAAACAA