RetrogeneDB ID:

retro_cjac_3814

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:GL284765.1:5158..5857(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCJAG00000003923
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:FAM204A
Ensembl ID:ENSCJAG00000019565
Aliases:None
Description:family with sequence similarity 204, member A [Source:HGNC Symbol;Acc:25794]


Retrocopy-Parental alignment summary:






>retro_cjac_3814
ATGTGGAGTGGGCTGCTACCTCCTGGCCTAAATGAAGTGATGTTGAGTCAAACTCTGAAGATGAAGCTACGTTGGAGAAC
TCTGTACTGAACTTACAGGAAGATAAAGAGGATGGGAGCATCAGTAAAACAGAAATCACAGATTTTTCAACAGATGAACC
AAAAACTGAAAAGGGAGTCAAATGTAAATGCCTATGAAGAGTGTCCCTCTGGAATTCCCATAGATATGTGGAATAAATTT
CAAGAATTGCATAAAAAACATTCTGAACAGAAAAAAACAACCTCAAGATTCAGAGGGGAAAAAAGAAAACGCTCCAGAAA
AGATAAATTGAAGAATGAGAAAAAATTTCATAGTGAAGAGTCCTCAAATGAAACCCAGTGGAAGAAGCTTACTCAGTATT
CTGGAGTCAATGATAGATTTGACCCTCCTGTTAAAAGGAAAAAAGTTGAGAAGTCAGGCCTTGAAAAGAGGATAGACCAG
GCTGTGGGTGAGTGGAATGTTGAGAAGGCTGAGGAACTTAGCAACCACCTAGCTACTCGAGAGCTTGGTGTCAAAATTGC
CAAAGCAGTTGCCTGCCACAACTTTGTAAAATCCAAAAAGGAGGTTGAAAATTCACAGGCTGCCCAAAAAAAGAAGAAAC
TCGCATGGGGGTTTGAAGCAAAGAAGAGATGGGAAACCAAAAGCAACATGGGATATATG

ORF - retro_cjac_3814 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 94.04 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMWSGLLPPGLNE-SDVESNSEDEATLENSGLNLQEDKEDGSISKTEITDFSTDEPKTE-MESNVNAYEEC
MWSGLLPPGLNE.SDVESNSEDEATLENS.LNLQEDKEDGSISKTEITDFSTDEPKTE..ESNVNAYEEC
RetrocopyMWSGLLPPGLNE<SDVESNSEDEATLENSVLNLQEDKEDGSISKTEITDFSTDEPKTE>RESNVNAYEEC
ParentalPSGIPIDMWNKFQELHKKHSEQKNTTSRFRGKKRKRSRKDKLKNEKESHSEESSNETQWKELTQYFGVND
PSGIPIDMWNKFQELHKKHSEQK.TTSRFRG.KRKRSRKDKLKNEK..HSEESSNETQWK.LTQY.GVND
RetrocopyPSGIPIDMWNKFQELHKKHSEQKKTTSRFRGEKRKRSRKDKLKNEKKFHSEESSNETQWKKLTQYSGVND
ParentalRFDPPVKRKKVEKSGLEKRIDQAVDEWNIEKAEELSNHLATRELGVKIAKAVACHNFVKAKKEVENSQAA
RFDPPVKRKKVEKSGLEKRIDQAV.EWN.EKAEELSNHLATRELGVKIAKAVACHNFVK.KKEVENSQAA
RetrocopyRFDPPVKRKKVEKSGLEKRIDQAVGEWNVEKAEELSNHLATRELGVKIAKAVACHNFVKSKKEVENSQAA
ParentalRKKKKLAWGFEAKKRWETKSNMGYM
.KKKKLAWGFEAKKRWETKSNMGYM
RetrocopyQKKKKLAWGFEAKKRWETKSNMGYM

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






RNA-Seq - click to see more details

(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 .95 RPM 14 .91 RPM
SRP051959_heart 1 .05 RPM 22 .36 RPM
SRP051959_kidney 1 .20 RPM 30 .28 RPM
SRP051959_liver 0 .67 RPM 16 .57 RPM
SRP051959_lung 1 .98 RPM 23 .18 RPM
SRP051959_lymph_node 2 .31 RPM 28 .77 RPM
SRP051959_skeletal_muscle 0 .33 RPM 18 .56 RPM
SRP051959_spleen 1 .39 RPM 25 .50 RPM

ChIP-Seq - click to see more details

Callithrix jacchus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_cjac_3814 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_3814 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_3814 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 24 parental genes, and 47 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG0000001019912 retrocopies
retro_chof_1296, retro_chof_1713, retro_chof_1977, retro_chof_2137, retro_chof_2367, retro_chof_2436, retro_chof_2558, retro_chof_2685, retro_chof_590, retro_chof_639, retro_chof_698, retro_chof_832,
Callithrix jacchus ENSCJAG00000019565 1 retrocopy
retro_cjac_3814 ,
Cavia porcellus ENSCPOG000000027471 retrocopy
retro_cpor_1356,
Dasypus novemcinctus ENSDNOG000000013832 retrocopies
retro_dnov_138, retro_dnov_167,
Dipodomys ordii ENSDORG000000020741 retrocopy
retro_dord_413,
Echinops telfairi ENSETEG000000038552 retrocopies
retro_etel_1021, retro_etel_944,
Homo sapiens ENSG000001656691 retrocopy
retro_hsap_491,
Gorilla gorilla ENSGGOG000000105661 retrocopy
retro_ggor_460,
Loxodonta africana ENSLAFG000000167744 retrocopies
retro_lafr_1079, retro_lafr_332, retro_lafr_369, retro_lafr_923,
Macropus eugenii ENSMEUG000000026741 retrocopy
retro_meug_606,
Myotis lucifugus ENSMLUG000000274541 retrocopy
retro_mluc_29,
Macaca mulatta ENSMMUG000000127411 retrocopy
retro_mmul_722,
Monodelphis domestica ENSMODG000000093783 retrocopies
retro_mdom_112, retro_mdom_1258, retro_mdom_38,
Mustela putorius furoENSMPUG000000032391 retrocopy
retro_mputfur_1400,
Oryctolagus cuniculus ENSOCUG000000051501 retrocopy
retro_ocun_1487,
Otolemur garnettii ENSOGAG000000285411 retrocopy
retro_ogar_1610,
Procavia capensis ENSPCAG000000115011 retrocopy
retro_pcap_400,
Pongo abelii ENSPPYG000000026941 retrocopy
retro_pabe_242,
Pan troglodytes ENSPTRG000000029841 retrocopy
retro_ptro_370,
Pteropus vampyrus ENSPVAG000000046212 retrocopies
retro_pvam_366, retro_pvam_776,
Sorex araneus ENSSARG000000008193 retrocopies
retro_sara_258, retro_sara_323, retro_sara_541,
Sarcophilus harrisii ENSSHAG000000116013 retrocopies
retro_shar_155, retro_shar_412, retro_shar_476,
Tarsius syrichta ENSTSYG000000091471 retrocopy
retro_tsyr_518,
Tursiops truncatus ENSTTRG000000033511 retrocopy
retro_ttru_1322,


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