Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgatgctcattcttttgggacagagaaatttgcacgctccatgtaaaaatgttgcatattaattgtcaaaccatgttaattatgcataccatcattgcagTCTTCTGCAAGCAGCAATCGGAGCGTTCTCTACAGTCTTTCCTGACTACCAGGAGAGGATTGCTAGGCATGAAGCTGCTCATTTCCTAG

Basic information

species Zea mays
transcript GRMZM2G004352_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G004352_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os04g54640.1 (Oryza sativa), 3'ss of exon 5
tgatgctcattcttttgggacagagaaattt--gcacgctccatgtaaaaatgttgcatattaattgtcaaaccatgttaattatgcataccatcattgcagTCTTCTGCAAGCAGCAATCGGAGCGTTCTCTACAGTCTTTCCTGACTACCAGGAGAGGATTGCTAGGCATGAAGCTGCTCATTTCCTAG
  |||      |   |   ||       |||  | |  ||| ||| ||| ||||||||  || ||  | ||   ||  ||||| | ||| |||||||  ||||||||||||||||||||| || || || || || || ||||||||||| |||||||| ||||||||||||||||||||||||||  | |
--atggcatgacaaataacactatctgttttatgaatactcaatgaaaatatgttgcaactttatcatgaatagattgtaattttccattccatcatcacagTCTTCTGCAAGCAGCAATTGGTGCATTTTCAACTGTTTTTCCTGACTATCAGGAGAGAATTGCTAGGCATGAAGCTGCTCATTTTTTGG

upper sequence: GRMZM2G004352_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv07s0031g01560.t01 (Vitis vinifera), 3'ss of exon 5
----------------------------------tgatgctcattcttttggga-cagagaaatttgcacgctccat--------gtaaaaatgttgc--atattaattgtcaaaccatgttaattatgcataccatcattgcagTCTTCTGCAAGCAGCAATCGGAGCGTTCTCTACAGTCTTTCCTGACTACCAGGAGAGGATTGCTAGGCATGAAGCTGCTCATTTCCTAG
                                  |   |   ||| | || ||| ||    || |||||    | ||        |  | | ||| |   | |||||   ||| | |    | |   |   || |  |  || || ||||| || |  || || ||||  || ||  || | |||||||| || ||||||||||||||||| |||||||| || |||||  |||
gtaagcgttaaatctgtccatgatacaagttacatttagaggattgtgttaggatcatgttaagttgcatatccaataattgagagacagagtgtagagaagattaacc-tcagaactcactgacactctttatctgctctgtagGCTTCTTCAGGTTGCCATTGGAGGATTTTCATCATTTTTTCCTGATTATCAGGAGAGGATTGCTAGACATGAAGCAGCCCATTTTTTAG
















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|50329898|gb|CO525024.1|CO525024
EST:     ATTGGAAGCATTTCATTGATCGTATTGGCTGTCGGAAGCGTCGCTCCAGG                         TCTTCTGCAAGCAGCAATCGGAGCGTTCTCTACAGTCTTTCCTGACTACCA
genomic: ATTGGAAGCATTTCATTGATCGTATTGGCTGTCGGAAGCGTCGCTCCAGGgtacgtgttt ... atcattgcagTCTTCTGCAAGCAGCAATCGGAGCGTTCTCTACAGTCTTTCCTGACTACCA
EST: gi|148954649|gb|EC900096.2|EC900096
EST:     ATTGGAAGCATTTCATTGATCGTATTGGCTGTCGGAAGCGTCGCTCCAGG                         TCTTCTGCAAGCAGCAATCGGAGCGTTCTCTACAGTCTTTCCTGACTACCA
genomic: ATTGGAAGCATTTCATTGATCGTATTGGCTGTCGGAAGCGTCGCTCCAGGgtacgtgttt ... atcattgcagTCTTCTGCAAGCAGCAATCGGAGCGTTCTCTACAGTCTTTCCTGACTACCA
EST: gi|149084909|gb|EE174419.2|EE174419
EST:     ATTGGAAGCATTTCATTGATCGTATTGGCTGTCGGAAGCGTCGCTCCAGG                         TCTTCTGCAAGCAGCAATCGGAGCGTTCTCTACAGTCTTTCCTGACTACCA
genomic: ATTGGAAGCATTTCATTGATCGTATTGGCTGTCGGAAGCGTCGCTCCAGGgtacgtgttt ... atcattgcagTCTTCTGCAAGCAGCAATCGGAGCGTTCTCTACAGTCTTTCCTGACTACCA
EST: gi|211057978|gb|FL426568.1|FL426568
EST:     TTG-AAGCATTTCATTGATCGTATTGGCTGGTCGGA-GCGTCGCTCCAGG                         TCTTCTGCA-GCAGCNATCGGAGCGT-CTCTACAGTCTTTC-TGACTACCA
genomic: TTGGAAGCATTTCATTGATCGTATTGGCTG-TCGGAAGCGTCGCTCCAGGgtacgtgttt ... atcattgcagTCTTCTGCAAGCAGCAATCGGAGCGTTCTCTACAGTCTTTCCTGACTACCA
EST: gi|76010526|gb|DT937696.1|DT937696
EST:     ATTGGAAGCATTTCATTGATCGTATTGGCTGTCGGAAGCGTCGCTCCAGG                         ACTTCTGCAAGCAGCAATCGGAGCGTTCTCTACAGTCTTTCCTGACTACCA
genomic: ATTGGAAGCATTTCATTGATCGTATTGGCTGTCGGAAGCGTCGCTCCAGGgtacgtgttt ... atcattgcagTCTTCTGCAAGCAGCAATCGGAGCGTTCTCTACAGTCTTTCCTGACTACCA
EST: gi|71313543|gb|DR793346.1|DR793346
EST:     ATTGGAAGCATTTCATTGATCGTATTGGCTGTCGGAAGCGTCGCTCCAGG                         TCTTCTGCAAGCAGCAATCGGAGCGTTCTCTACAGTCTTTCCTGACTACCA
genomic: ATTGGAAGCATTTCATTGATCGTATTGGCTGTCGGAAGCGTCGCTCCAGGgtacgtgttt ... atcattgcagTCTTCTGCAAGCAGCAATCGGAGCGTTCTCTACAGTCTTTCCTGACTACCA
EST: gi|37417290|gb|CF646298.1|CF646298
EST:     ATTGGAAGCATTTCATTGATCGTATTGGCTGTCGGAAGCGTCGCTCCAGG                         TCTTCTGCAAGCAGCAATCGGAGCGTTCTCTACAGTCTTTCCTGACTACCA
genomic: ATTGGAAGCATTTCATTGATCGTATTGGCTGTCGGAAGCGTCGCTCCAGGgtacgtgttt ... atcattgcagTCTTCTGCAAGCAGCAATCGGAGCGTTCTCTACAGTCTTTCCTGACTACCA
EST: gi|149100298|gb|EE186363.2|EE186363
EST:     ATTGGAAGCATTTCATTGATCGTATTGGCTGTCGGAAGCGTCGCTCCAGG                         TCTTCTGCAAGCAGCAATCGGAGCGTTCTCTACAGTCTTTCCTGACTACCA
genomic: ATTGGAAGCATTTCATTGATCGTATTGGCTGTCGGAAGCGTCGCTCCAGGgtacgtgttt ... atcattgcagTCTTCTGCAAGCAGCAATCGGAGCGTTCTCTACAGTCTTTCCTGACTACCA
EST: gi|148930743|gb|EC873038.2|EC873038
EST:     ATTGGAAGCATTTCATTGATCGTATTGGCTGTCGGAAGCGTCGCTCCAGG                         TCTTCTGCAAGCAGCAATCGGAGCGTTCTCTACAGTCTTTCCTGACTACCA
genomic: ATTGGAAGCATTTCATTGATCGTATTGGCTGTCGGAAGCGTCGCTCCAGGgtacgtgttt ... atcattgcagTCTTCTGCAAGCAGCAATCGGAGCGTTCTCTACAGTCTTTCCTGACTACCA
EST: gi|71317339|gb|DR795363.1|DR795363
EST:     ATTGGAAGCATTTCATTGATCGTATTGGCTGTCGGAAGCGTCGCTCCAGG                         TCTTCTGCAAGCAGCAATCGGAGCGTTCTCTACAGTCTTTCCTGACTACCA
genomic: ATTGGAAGCATTTCATTGATCGTATTGGCTGTCGGAAGCGTCGCTCCAGGgtacgtgttt ... atcattgcagTCTTCTGCAAGCAGCAATCGGAGCGTTCTCTACAGTCTTTCCTGACTACCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaatgttgcatattaattgtcaaaccatgttaattatgcataccatcattgcagTCTTCTGCAAGCAGCAATCGGAGCGTTCTCTACAGTCTTTCCTGACTACCAGGAGAGGATTGCTAGGCATGAAGCTGCTCATTTCCTAG
          atattaattgtcaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgatgctcattcttttgggacagagaaatttgcacgctccatgtaaaaatgttgcatattaattgtcaaaccatgttaattatgcataccatcattgcagTCTTCTGCAAGCAGCAATCGGAGCGTTCTCTACAGTCTTTCCTGACTACCAGGAGAGGATTGCTAGGCATGAAGCTGCTCATTTCCTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT