RetrogeneDB ID:

retro_cfam_1120

Retrocopy
location
Organism:Dog (Canis familiaris)
Coordinates:23:15889873..15890541(-)
Located in intron of:ENSCAFG00000005488
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:FAM60A
Ensembl ID:ENSCAFG00000010685
Aliases:None
Description:family with sequence similarity 60, member A [Source:HGNC Symbol;Acc:30702]


Retrocopy-Parental alignment summary:






>retro_cfam_1120
GAATAAAAGATGTTTAGTTTTACAAACCAAAGATGTGCTGAAGTATAGAGGGCTGCTCTATTTGCAGAGCTAAGTTCTGC
ACTTCTCGGTTTAGTTATAGTAAATAATGAAAGGACTTTCAGAGCTGCAGTTTACAGCTACTCAAGACTTCAGAAAACTT
TTGCAATAGCTGAGTACTATTATGAAAAGATAGAAAAAGCTACCAGCAGGATAAAAAAACAAAACAACTGGAATCATGTT
GTAGGCTCAAGGGCAGGACCCCAGTCTAAACTCTGTATCAAAACCAAAGAAAGTGTAAAGTATCTGGGAAAAAGATAAAG
AAGCAACTAGATTGGTTAACTACAGGAAGAGTTTCAACTTCACGGCCCTGATGCCCACCATACCACCTCAATTACCTCTT
CAACTCAGTCTCCCTGTGCATTTACCAGTCAGATGATGACTTTGATACAGAAATGGCTTCTGGTTCAAACAACACACCTA
CCTTTTCTTTGTAATCTCACGTGTTGGAAAAAGCAGAAACTATGTTGTGGGTTTTAACTATAAAAGGCACTTTGGGGAAG
TCCTTGACACCCACCTATTTAATAAGCCTTGCTTCAGCAGTAAGAAAGCAGTTTCTGAGAAGCCGGAGAAGTGTGGTACT
AGAGCCTCTACCCATTTCCATTGAGGAG

ORF - retro_cfam_1120 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 53.88 %
Parental protein coverage: 97.81 %
Number of stop codons detected: 12
Number of frameshifts detected: 6


Retrocopy - Parental Gene Alignment:

ParentalEEKMFGF-HKPKMYRSIEGCCICRAKSSSSRFTDSKRYEKDFQSCFGLHETRSGDICNACVLL-VKRWKK
E.KMF.F..KPKM..SIEGC.ICRAK...SRF..SK....DFQSC.......S...CN..VLL..KR.KK
RetrocopyE*KMFSF<YKPKMC*SIEGCSICRAKFCTSRFSYSK**K-DFQSCSLQLLKTSENFCNS*VLL<MKR*KK
ParentalLPAGSKKNWNHVVDARAG--PSLKTTLKPKKVKTL-SGNRIKSNQISKLQKEFKRHNSDAHSTTSSASPA
LPAG.K...........G..PSL....KPKKV.....G.R..SN.I..LQ.EF..H..DAH.TTS..S..
RetrocopyLPAG*KNKTTGIML*AQGQDPSLNSVSKPKKV*SI<LGKR*RSN*IG*LQEEFQLHGPDAHHTTSITSST
ParentalQSPCYSN-QSDDGSDTEMASGSNRTPVFS-FLDLTYWKRQKICCGIIYKGRFGEVLIDTHLF-KPCCSNK
QSPC....QSDD..DTEMASGSN.TP.FS.F......K......G..YK..FGEVL.DTHLF.KPC.S.K
RetrocopyQSPCAFT<QSDDDFDTEMASGSNNTPTFS<FVISRVGKSRNYVVGFNYKRHFGEVL-DTHLFNKPCFSSK
ParentalKAAAEKPEEQGP-EPLPISTQE
KA..EKPE..G..EPLPIS..E
RetrocopyKAVSEKPEKCGT>EPLPISIEE

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
SRP012049_cerebellum 0 .08 RPM 1 .97 RPM
SRP017611_brain 0 .08 RPM 0 .48 RPM
SRP017611_kidney 0 .00 RPM 4 .62 RPM
SRP017611_liver 0 .07 RPM 0 .73 RPM

ChIP-Seq - click to see more details

Canis familiaris was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_cfam_1120 retrocopy.

TSS - click to see more details

Canis familiaris was not studied using FANTOM5 data.

Lab - click to see more details

retro_cfam_1120 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cfam_1120 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Equus caballus retro_ecab_385
Parental genes homology:
Parental genes homology involve 24 parental genes, and 70 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000011611 retrocopy
retro_btau_1020,
Canis familiaris ENSCAFG00000010685 4 retrocopies
retro_cfam_1120 , retro_cfam_1552, retro_cfam_1692, retro_cfam_1837,
Choloepus hoffmanni ENSCHOG0000000719317 retrocopies
retro_chof_109, retro_chof_1108, retro_chof_1136, retro_chof_1255, retro_chof_1614, retro_chof_1689, retro_chof_1770, retro_chof_1971, retro_chof_2126, retro_chof_2493, retro_chof_2576, retro_chof_2587, retro_chof_453, retro_chof_511, retro_chof_856, retro_chof_979, retro_chof_998,
Callithrix jacchus ENSCJAG000000012153 retrocopies
retro_cjac_1072, retro_cjac_3154, retro_cjac_3289,
Dasypus novemcinctus ENSDNOG000000168732 retrocopies
retro_dnov_1674, retro_dnov_2668,
Equus caballus ENSECAG000000096552 retrocopies
retro_ecab_287, retro_ecab_385,
Erinaceus europaeus ENSEEUG000000126172 retrocopies
retro_eeur_350, retro_eeur_372,
Echinops telfairi ENSETEG000000028882 retrocopies
retro_etel_1087, retro_etel_427,
Felis catus ENSFCAG000000089554 retrocopies
retro_fcat_1311, retro_fcat_1339, retro_fcat_58, retro_fcat_965,
Homo sapiens ENSG000001391463 retrocopies
retro_hsap_1928, retro_hsap_1945, retro_hsap_4029,
Gorilla gorilla ENSGGOG000000154843 retrocopies
retro_ggor_1405, retro_ggor_1415, retro_ggor_2704,
Microcebus murinus ENSMICG000000034602 retrocopies
retro_mmur_1176, retro_mmur_409,
Myotis lucifugus ENSMLUG000000098273 retrocopies
retro_mluc_1663, retro_mluc_1672, retro_mluc_765,
Macaca mulatta ENSMMUG000000091552 retrocopies
retro_mmul_1074, retro_mmul_2324,
Mus musculus ENSMUSG000000399854 retrocopies
retro_mmus_1234, retro_mmus_1471, retro_mmus_1557, retro_mmus_3331,
Nomascus leucogenys ENSNLEG000000164871 retrocopy
retro_nleu_1213,
Oryctolagus cuniculus ENSOCUG000000086181 retrocopy
retro_ocun_1176,
Otolemur garnettii ENSOGAG000000089274 retrocopies
retro_ogar_1253, retro_ogar_1762, retro_ogar_2117, retro_ogar_251,
Pongo abelii ENSPPYG000000043962 retrocopies
retro_pabe_1592, retro_pabe_3309,
Rattus norvegicus ENSRNOG000000460481 retrocopy
retro_rnor_2858,
Rattus norvegicus ENSRNOG000000499432 retrocopies
retro_rnor_1121, retro_rnor_2917,
Sarcophilus harrisii ENSSHAG000000062611 retrocopy
retro_shar_670,
Ictidomys tridecemlineatus ENSSTOG000000070971 retrocopy
retro_itri_16,
Tursiops truncatus ENSTTRG000000084653 retrocopies
retro_ttru_1162, retro_ttru_1498, retro_ttru_984,


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