RetrogeneDB ID:

retro_cjac_2893

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:7:69382213..69382668(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPS18
Ensembl ID:ENSCJAG00000021650
Aliases:None
Description:ribosomal protein S18 [Source:HGNC Symbol;Acc:10401]


Retrocopy-Parental alignment summary:






>retro_cjac_2893
ATGTCTCTAGTGATCCCTGAAAAGTTCCAGCATATTTTGTGAGTACTCAACACCCACATCGATGGGCGGCAGAAAATAGC
CTTTGCCATCACTGCCATTAAGGGTGTGGCTAAAGATACGCTCATGTGGTGTTGAGGAAAGCAGACATTGGCCTCACCAA
GAAGGCAGGAGAACTCACTGAGGATGAGGTAGAACGTGCAATCACCATTATGCAGAATCCACTTCAGTACAAGATCCCAG
ACTGGTTCTTGGACAGACGGAAAGATGTAAAGGATGGGAAATATAGCCAGGTCCTAGCCAATGGTGTGGACAACAAGATC
CGTGAAGACTTGGAGAGACTGAAGAAGATTCAGGCCCATGGAGGGCTGCGCCACTTCTGGGGCCTTTGGGTCCAAGGCCA
GCACACCAAGACCACTGGCCGCCGTGGCCGCACCATGGGTGTGTCCACAAAGAAA

ORF - retro_cjac_2893 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 86.93 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMSLVIPEKFQHILRVLNTNIDGRRKIAFAITAIKGVGR-RYAHVVLRKADIDLTKRAGELTEDEVERVIT
MSLVIPEKFQHIL.VLNT.IDGR.KIAFAITAIKGV...RYAHVVLRKADI.LTK.AGELTEDEVER.IT
RetrocopyMSLVIPEKFQHIL*VLNTHIDGRQKIAFAITAIKGVAK<RYAHVVLRKADIGLTKKAGELTEDEVERAIT
ParentalIMQNPRQYKIPDWFLNRQKDVKDGKYSQVLANGLDNKLREDLERLKKIRAHRGLRHFWGLRVRGQHTKTT
IMQNP.QYKIPDWFL.R.KDVKDGKYSQVLANG.DNK.REDLERLKKI.AH.GLRHFWGL.V.GQHTKTT
RetrocopyIMQNPLQYKIPDWFLDRRKDVKDGKYSQVLANGVDNKIREDLERLKKIQAHGGLRHFWGLWVQGQHTKTT
ParentalGRRGRTVGVSKKK
GRRGRT.GVS.KK
RetrocopyGRRGRTMGVSTKK

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
SRP051959_colon 0 .00 RPM 222 .14 RPM
SRP051959_heart 0 .02 RPM 143 .92 RPM
SRP051959_kidney 0 .00 RPM 183 .90 RPM
SRP051959_liver 0 .00 RPM 335 .65 RPM
SRP051959_lung 0 .00 RPM 204 .16 RPM
SRP051959_lymph_node 0 .00 RPM 463 .34 RPM
SRP051959_skeletal_muscle 0 .00 RPM 240 .81 RPM
SRP051959_spleen 0 .00 RPM 284 .83 RPM
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2893 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2893 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_2893 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 23 parental genes, and 139 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000026482 retrocopies
Callithrix jacchus ENSCJAG000000103561 retrocopy
Callithrix jacchus ENSCJAG00000021650 5 retrocopies
Dasypus novemcinctus ENSDNOG0000001208413 retrocopies
Erinaceus europaeus ENSEEUG000000102978 retrocopies
Homo sapiens ENSG000002315002 retrocopies
Gorilla gorilla ENSGGOG000000065715 retrocopies
Loxodonta africana ENSLAFG000000321731 retrocopy
Macropus eugenii ENSMEUG0000001677011 retrocopies
Myotis lucifugus ENSMLUG000000073602 retrocopies
Macaca mulatta ENSMMUG000000038671 retrocopy
Monodelphis domestica ENSMODG000000142104 retrocopies
Oryctolagus cuniculus ENSOCUG000000105461 retrocopy
Otolemur garnettii ENSOGAG000000062257 retrocopies
Pongo abelii ENSPPYG0000002595314 retrocopies
Pan troglodytes ENSPTRG000000180391 retrocopy
Pteropus vampyrus ENSPVAG000000019026 retrocopies
Rattus norvegicus ENSRNOG000000285054 retrocopies
Sarcophilus harrisii ENSSHAG000000068572 retrocopies
Sarcophilus harrisii ENSSHAG000000086581 retrocopy
Sus scrofa ENSSSCG000000015025 retrocopies
Tupaia belangeri ENSTBEG0000001270840 retrocopies
Tursiops truncatus ENSTTRG000000043023 retrocopies



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