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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agcatggatacctctttaaccttttgcaatctagccatttgtgtctaaaactggaaactatgcaatattaatcaatgtcctctttcatatggcggcacagGACATATGGAAGATCCGTCTTCAACTTACTAAGCCGGTGACATGGCCTCCGCTTGTTTGGGGAGTTCTCTGTGGAGCAGCTGCCTCTG

Basic information

species Zea mays
transcript GRMZM2G162672_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G162672_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os05g28200.1 (Oryza sativa), 3'ss of exon 3
agcatggatacctctttaaccttttgcaatctagccatttgtgtcta-aaactggaaactatgcaatattaatcaatgtcctctttcatatggcg-gcacagGACATATGGAAGATCCGTCTTCAACTTACTAAGCCGGTGACATGGCCTCCGCTTGTTTGGGGAGTTCTCTGTGGAGCAGCTGCCTCTG
   ||    | || |||  | |||||||||| |    ||  ||| |  ||||    ||   |  | |  ||||||||   |||||||| |||| |   | |||||||||||||||| || ||||||||||||||||| |||||||||||||||||||| |||||||| || |||||||||||||||||||
--gatatgcatctttttctctttttgcaatcaatatgttcatgtatggaaacaactaatgctatattgctaatcaattaactctttcacatggtgcatatagGACATATGGAAGATTCGCCTTCAACTTACTAAGCCAGTGACATGGCCTCCGCTTGTATGGGGAGTGCTTTGTGGAGCAGCTGCCTCTG

upper sequence: GRMZM2G162672_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA18G43310.1 (Glycine max), 3'ss of exon 3
-agcatggatacctctttaaccttttgcaatctagccatttg-tgtctaaaactggaaactatgcaatattaatcaatgtcctctttcatatggcggcacagGACATATGGAAGATCCGTCTTCAACTTACTAAGCCGGTGACATGGCCTCCGCTTGTTTGGGGAGTTCTCTGTGGAGCAGCTGCCTCTG
       | ||||   | |   |     |||  |   ||  | |  ||     || ||| |||    ||||    |||    |   | ||||   ||  ||| | |  |||||||| |||||||||||||| ||||| || || ||||||||  | |||||||| ||  | |||||||| ||||| ||||
ttatgcagttaccagataactgtaaaataatgcatttatcagataactgtttttgaaaagtatttg-tatttcataattgattgggtaatata-tggtgcagAATAAGTGGAAGATTCGTCTTCAACTTACAAAGCCAGTCACTTGGCCTCCATTAGTTTGGGGTGTAGTTTGTGGAGCTGCTGCTTCTG

upper sequence: GRMZM2G162672_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA07G18470.1 (Glycine max), 3'ss of exon 3
agcatggatacctctttaaccttttgcaatctagccatttg-tgtctaaaactggaaactatgcaatattaatcaatgtcctctttcatatggcggcacagGACATATGGAAGATCCGTCTTCAACTTACTAAGCCGGTGACATGGCCTCCGCTTGTTTGGGGAGTTCTCTGTGGAGCAGCTGCCTCTG
      | ||||   | |   |     |||  ||  ||| | |  ||     |  |||  ||    | ||  | |||    |   | ||||   ||  ||| | | ||||||||| ||||||||||| || ||||| || || ||||||||| | |||||||| ||  | ||||| || |||||||| |
tatgcagttaccagataactgtaaattaatgcagttattagataacttttttttaaaaaaatattgtgtttcttaattgattgggtaatata-tggtgcagAATAAATGGAAGATTCGTCTTCAACTCACAAAGCCTGTCACTTGGCCTCCGTTAGTTTGGGGTGTAGTTTGTGGTGCTGCTGCCTCGG

upper sequence: GRMZM2G162672_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT3G51820.1 (Arabidopsis thaliana), 3'ss of exon 3
-------------------------------------------------------------agcatggatacctctttaac-----------cttttgcaatctagccatttgt---gtctaaaactg----gaaactatgcaatattaatcaat----gtcctctttcatatggcg-gcacagGACATATGGAAGATCCGTCTTCAACTTACTAAGCCGGTGACATGGCCTCCGCTTGTTTGGGGAGTTCTCTGTGGAGCAGCTGCCTCTG
                                                             ||  | |  |  |   ||             ||||||    | || | | | |   |  || || ||    |||| | |    | |||   ||     ||    | | ||||   |    ||| | | ||||||||| |||||||| ||||| || || || || |||||||| || |||||||||||  ||||||| || ||||| || |
gtaattttgttcatctcctcagaatcttttaaattatcatatttgtggataatgatgtgttagtttaggaattttcctactaaaggtaatctcttttgaggacaagtcttgtttttagcttagaaatgatgtgaaaatgttgtttgttagctaaaaagagtttgttgttatattctgtattcagAATAAATGGAAGATTCGTCTTCAGCTTACAAAACCAGTCACTTGGCCTCCACTGGTTTGGGGAGTCGTCTGTGGTGCTGCTGCTTCAG

upper sequence: GRMZM2G162672_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv08s0105g00590.t01 (Vitis vinifera), 3'ss of exon 3
-agcatggatacctctttaaccttttgcaatctagccatttg---tgtctaaaactggaaactatgcaatattaatcaatgtcctctttcatatggcggcacagGACATATGGAAGATCCGTCTTCAACTTACTAAGCCGGTGACATGGCCTCCGCTTGTTTGGGGAGTTCTCTGTGGAGCAGCTGCCTCTG
 ||  ||||    | |||     || | ||   |   |   |   | | | ||  |  ||| | |||||    | |  ||    |  ||  ||| | |   ||| | | ||||||||| |||||||||||||| ||||| || || ||||| ||| | |||||||||||  | |||||||| ||||| ||||
cagtttggaggtgtttttttttattagaaagacatttagcagaattatatgaagattaaaa-tctgcaactagagttgattgtatgatttgtattgtg---cagAATAAATGGAAGATTCGTCTTCAACTTACAAAGCCTGTTACTTGGCCCCCGTTGGTTTGGGGAGTGGTTTGTGGAGCTGCTGCTTCTG

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|149038823|gb|EE155536.2|EE155536
EST:     GCTCCAGTTTCAACCAGCTGCTCGGTATCAAGGGTGCTAAGCAAGAGAGC                         GACATATGGAAGATCCGTCTTCAACTTACTAAGCCGGTGACATGGCCTCCG
genomic: GCTCCAGTTTCAACCAGCTGCTCGGTATCAAGGGTGCTAAGCAAGAGAGCgtgagtcttc ... ggcggcacagGACATATGGAAGATCCGTCTTCAACTTACTAAGCCGGTGACATGGCCTCCG
EST: gi|211379068|gb|FL028409.1|FL028409
EST:     GCTCCAGTTTCAACCAGCTGCTCGGTATCAAGGGTGCTAAGCAAGAGAGC                         GACATATGGAAGATCCGTCTTCAACTTACTAAGCCGGTGACATGGCCTCCG
genomic: GCTCCAGTTTCAACCAGCTGCTCGGTATCAAGGGTGCTAAGCAAGAGAGCgtgagtcttc ... ggcggcacagGACATATGGAAGATCCGTCTTCAACTTACTAAGCCGGTGACATGGCCTCCG
EST: gi|211302748|gb|FL028408.1|FL028408
EST:     GCTCCAGTTTCAACCAGCTGCTCGGTATCAAGGGTGCTAAGCAAGAGAGC                         GACATATGGAAGATCCGTCTTCAACTTACTAAGCCGGTGACATGGCCTCCG
genomic: GCTCCAGTTTCAACCAGCTGCTCGGTATCAAGGGTGCTAAGCAAGAGAGCgtgagtcttc ... ggcggcacagGACATATGGAAGATCCGTCTTCAACTTACTAAGCCGGTGACATGGCCTCCG
EST: gi|61119511|gb|DN560472.1|DN560472
EST:     GCTCCAGTTTCAACCAGCTGCTCGGTATCAAGGGTGCTAAGCAAGAGAGC                         GACATATGGAAGATCCGTCTTCAACTTACTAAGCCGGTGACATGGCCTCCG
genomic: GCTCCAGTTTCAACCAGCTGCTCGGTATCAAGGGTGCTAAGCAAGAGAGCgtgagtcttc ... ggcggcacagGACATATGGAAGATCCGTCTTCAACTTACTAAGCCGGTGACATGGCCTCCG
EST: gi|78120047|gb|DV538431.1|DV538431
EST:     GCTCCAGTTTCAACCAGCTGCTCGGTATCAAGGGTGCTAAGCAAGAGAGC                         GACATATGGAAGATCCGTCTTCAACTTACTAAGCCGGTGACATGGCCTCCG
genomic: GCTCCAGTTTCAACCAGCTGCTCGGTATCAAGGGTGCTAAGCAAGAGAGCgtgagtcttc ... ggcggcacagGACATATGGAAGATCCGTCTTCAACTTACTAAGCCGGTGACATGGCCTCCG
EST: gi|211379069|gb|FL028410.1|FL028410
EST:     GCTCCAGTTTCAACCAGCTGCTCGGTATCAAGGGTGCTAAGCAAGAGAGC                         GACATATGGAAGATCCGTCTTCAACTTACTAAGCCGGTGACATGGCCTCCG
genomic: GCTCCAGTTTCAACCAGCTGCTCGGTATCAAGGGTGCTAAGCAAGAGAGCgtgagtcttc ... ggcggcacagGACATATGGAAGATCCGTCTTCAACTTACTAAGCCGGTGACATGGCCTCCG
EST: gi|149080582|gb|EE169625.2|EE169625
EST:     GCTCCAGTTTCAACCAGCTGCTCGGTATCAAGGGTGCTAAGCAAGAGAGC                         GACATATGGAAGATCCGTCTTCAACTTACTAAGCCGGTGACATGGCCTCCG
genomic: GCTCCAGTTTCAACCAGCTGCTCGGTATCAAGGGTGCTAAGCAAGAGAGCgtgagtcttc ... ggcggcacagGACATATGGAAGATCCGTCTTCAACTTACTAAGCCGGTGACATGGCCTCCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaaactggaaactatgcaatattaatcaatgtcctctttcatatggcggcacagGACATATGGAAGATCCGTCTTCAACTTACTAAGCCGGTGACATGGCCTCCGCTTGTTTGGGGAGTTCTCTGTGGAGCAGCTGCCTCTG
                    tattaat  putative branch site (score: 2)
                  aatattaatcaatgt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agcatggatacctctttaaccttttgcaatctagccatttgtgtctaaaactggaaactatgcaatattaatcaatgtcctctttcatatggcggcacagGACATATGGAAGATCCGTCTTCAACTTACTAAGCCGGTGACATGGCCTCCGCTTGTTTGGGGAGTTCTCTGTGGAGCAGCTGCCTCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC