RetrogeneDB ID: retro_cfam_2055

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: X:32149236..32149859(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: PRELID1
• Ensembl ID: ENSCAFG00000016443
• Aliases: None
• Description: PRELI domain containing 1 [Source:HGNC Symbol;Acc:30255]

Sequence

>retro_cfam_2055
ATGGTGAAGTATTTCCTGGGCCAGAGCATGCTCTGGAGTTCCTGGGACCAAGTGTTCACTACCTTCTGGCAGTGATACCC
AAATCCCTATAGCAAACGTGTCTTGACGGAAGACATTGTGCACCGGGAGGTGAACCCTGACCAGAAACTCCTGTCCCGGC
GTCTCCTGACCAAGACCATCAGGATGCCTCGCTGGGCTGCGTGACTATTTCCTGCCAATGTTGCTCACTCAGGGTACATC
CTGGAGGATTCTACTGTGGACCACAGAACCAGACCATGACCACCTTCACCTGGAACATCAACTGATGGCTGATGGTGGTG
GAGGAACGATGTGTTTACTGTGTGAATTCTGCTAACAGTGGCTGGACCGAAATCTGCCAGGAAGCCTGGGTCTCCTCTAG
GTTATTTGGTGTCTCCAGAGCTGTCCAGAAATTTGGTCTTGCCTGGTTCAAAAGCAACGTGACCAAGACAATGAAGGGCT
TTGAACATATCTTGGCCAAGCTGCAAGGTGAGGCCCCTTCCAAAACCTTTGTTGAGACAGCCAAGGAAGCCAAGGAGAAG
GCAAAGGAGATGGCACTGGCAGCTACAGAGAAGGCCAAGGACCTTGCCAGCAAGGCCACCACC

Alignment

ORF - retro_cfam_2055 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.62 %
• Parental protein coverage: 95.43 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MVKYFLGQSVLRSSWDQVFAAFWQRYPNPYSKHVLTEDIVHREVTPDQKLLSRRLLTKTNRMPRWAERLF
          MVKYFLGQS.L.SSWDQVF..FWQ.YPNPYSK.VLTEDIVHREV.PDQKLLSRRLLTKT.RMPRWA..LF
Retrocopy MVKYFLGQSMLWSSWDQVFTTFWQ*YPNPYSKRVLTEDIVHREVNPDQKLLSRRLLTKTIRMPRWAA*LF

Parental  PANVAHSVYILEDSIVD-PQNQTMTTFTWNINHARLMVVEERCVYCVNSDNSGWTEIRREAWVSSSLFGV
          PANVAHS.YILEDS.VD.PQNQTMTTFTWNIN...LMVVEERCVYCVNS.NSGWTEI..EAWVSS.LFGV
Retrocopy PANVAHSGYILEDSTVD<PQNQTMTTFTWNIN*W-LMVVEERCVYCVNSANSGWTEICQEAWVSSRLFGV

Parental  SRAVQEFGLARFKSNVTKTMKGFEYILAKLQGEAPSKTLVETAKEAKEKAKETALAATEKAKDLASKAAT
          SRAVQ.FGLA.FKSNVTKTMKGFE.ILAKLQGEAPSKT.VETAKEAKEKAKE.ALAATEKAKDLASKA.T
Retrocopy SRAVQKFGLAWFKSNVTKTMKGFEHILAKLQGEAPSKTFVETAKEAKEKAKEMALAATEKAKDLASKATT

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP012049_cerebellum	0.21 RPM	26.25 RPM
SRP017611_brain	0.16 RPM	18.66 RPM
SRP017611_kidney	0.07 RPM	88.42 RPM
SRP017611_liver	0.00 RPM	58.66 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_2055 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_2055 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_2055 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 61 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005009	2 retrocopies	retro_btau_1727, retro_btau_962,
Canis familiaris	ENSCAFG00000016443	2 retrocopies	retro_cfam_2055 , retro_cfam_349,
Callithrix jacchus	ENSCJAG00000006953	5 retrocopies	retro_cjac_1131, retro_cjac_1689, retro_cjac_2401, retro_cjac_3359, retro_cjac_835,
Homo sapiens	ENSG00000169230	7 retrocopies	retro_hsap_1550, retro_hsap_2269, retro_hsap_249, retro_hsap_302, retro_hsap_3518, retro_hsap_3565, retro_hsap_579,
Gorilla gorilla	ENSGGOG00000011762	3 retrocopies	retro_ggor_2404, retro_ggor_302, retro_ggor_9,
Macropus eugenii	ENSMEUG00000001738	12 retrocopies	retro_meug_1194, retro_meug_1541, retro_meug_1618, retro_meug_1725, retro_meug_1726, retro_meug_2054, retro_meug_274, retro_meug_666, retro_meug_681, retro_meug_854, retro_meug_895, retro_meug_918,
Myotis lucifugus	ENSMLUG00000007008	2 retrocopies	retro_mluc_239, retro_mluc_64,
Macaca mulatta	ENSMMUG00000009046	2 retrocopies	retro_mmul_1822, retro_mmul_2457,
Monodelphis domestica	ENSMODG00000004804	3 retrocopies	retro_mdom_1529, retro_mdom_221, retro_mdom_596,
Mustela putorius furo	ENSMPUG00000012226	1 retrocopy	retro_mputfur_579,
Nomascus leucogenys	ENSNLEG00000012714	5 retrocopies	retro_nleu_1382, retro_nleu_2395, retro_nleu_2400, retro_nleu_803, retro_nleu_857,
Otolemur garnettii	ENSOGAG00000011455	4 retrocopies	retro_ogar_1352, retro_ogar_2025, retro_ogar_3006, retro_ogar_665,
Pongo abelii	ENSPPYG00000016086	7 retrocopies	retro_pabe_1283, retro_pabe_1696, retro_pabe_1699, retro_pabe_2907, retro_pabe_377, retro_pabe_409, retro_pabe_608,
Sus scrofa	ENSSSCG00000014042	4 retrocopies	retro_sscr_372, retro_sscr_794, retro_sscr_795, retro_sscr_811,
Tupaia belangeri	ENSTBEG00000006445	1 retrocopy	retro_tbel_3855,
Tursiops truncatus	ENSTTRG00000009571	1 retrocopy	retro_ttru_1886,