RetrogeneDB ID: retro_cfam_780

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 17:48765718..48766366(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NECAP1
• Ensembl ID: ENSCAFG00000013930
• Aliases: None
• Description: NECAP endocytosis associated 1 [Source:HGNC Symbol;Acc:24539]

Sequence

>retro_cfam_780
GCTACAGGCTGGAATTCAGGCCAGCCTACTTCTACTGGTCACCTCCAATCATTTTGAAAGGGAAGGTTGTCTATCAACTT
GAGTATAAAACATCACAGGAGCTCTTTGGGCACCAGTAGAAACAATATCCTATCATTACTGAGGAGATAGTGACAGATTC
CAGCTTCTACTGTGTAATCTGGTTCCAGAATGACAGTGGACATAGTGCTTTCATTGGCATTTACTTCATAGAGTAGGTGA
TGCCTTTGACTTTAATATCCTTCTACAAAACCACTTCAAGTGGGTAAAGCAAGTATCTAAGATGTCCAATGAATCTCAAC
AACTGGACATTCATCCCAAGTTGGATCTGGGCTTCAAGGAAGGACAGATCATCATATTGAGTAATAGGAACATTGCAACC
AAGAGATGATGGTTTTCTAAGCCCAGGACTGCAGGAGACTGCGGGCCCAAGTTTACTCCCAGCCCCATTTGGAGGAAAAG
CCCCTATCCTCTCCCCCATCCTCAGAGGATGCCATGAGCAATCATGTTGCACCCACCACCCATTCCAAATCTAACCAAGG
AGGCAATGACACAGATATCCTTCTAGGCTGGGCTTCTCCTACTCCTGTCATGACACCAGCTCCAGTCTCTGACTTGGAGA
GACTTTGG

Alignment

ORF - retro_cfam_780 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.71 %
• Parental protein coverage: 80.59 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  ASDWKLDQPDWTGRLRITSKGKIAYIKLEDK-VSGELFAQAPVE-QYPGIAVETVTDSSRYFVIRIQDGT
          A..W...QP..TG.L....KG....I.L..K...G.L.A..PVE.QYP.I..E.VTDSS.Y.VI..Q...
Retrocopy ATGWNSGQPTSTGHLQSF*KGRLS-INLSIK>ITGALWA--PVE>QYPIITEEIVTDSSFYCVIWFQNDS

Parental  GRSAFIGIGFTD-RGDAFDFNVSLQDHFKWVKQESEISKESQEMDNRPKLDLGFKEGQTIKLSIGNITTK
          G.SAFIGI.F....GDAFDFN..LQ.HFKWVKQ.S..S.ESQ..D..PKLDLGFKEGQ.I.LS..NI.TK
Retrocopy GHSAFIGIYFIE<VGDAFDFNILLQNHFKWVKQVSKMSNESQQLDIHPKLDLGFKEGQIIILSNRNIATK

Parental  KGGVSKPKTTG-AGGLSLLPPPPGGKVTI-PPPSSSVAISNHVT-PPPIP-KSNHGGSDADILLDLDSPA
          ....SKP.T.G...G.SLLP.P.GGK..I..PPSS..A.SNHV..PPPIP.KSN.GG.D.DILL...SP.
Retrocopy R*WFSKPRTAG>TAGPSLLPAPFGGKAPI>SPPSSEDAMSNHVA>PPPIP<KSNQGGNDTDILLGWASPT

Parental  PVPTSAPAPVSASNDLW
          PV.T..PAPVS....LW
Retrocopy PVMT--PAPVSDLERLW

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	0.00 RPM	43.85 RPM
SRP017611_brain	0.00 RPM	53.27 RPM
SRP017611_kidney	0.00 RPM	15.52 RPM
SRP017611_liver	0.07 RPM	5.87 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_780 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_780 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_780 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016989	1 retrocopy	retro_amel_1016,
Canis familiaris	ENSCAFG00000013930	1 retrocopy	retro_cfam_780 ,
Canis familiaris	ENSCAFG00000015895	1 retrocopy	retro_cfam_1864,
Choloepus hoffmanni	ENSCHOG00000008087	3 retrocopies	retro_chof_1692, retro_chof_1818, retro_chof_1913,
Dasypus novemcinctus	ENSDNOG00000014778	2 retrocopies	retro_dnov_613, retro_dnov_986,
Homo sapiens	ENSG00000089818	1 retrocopy	retro_hsap_3839,
Gorilla gorilla	ENSGGOG00000010233	1 retrocopy	retro_ggor_2585,
Loxodonta africana	ENSLAFG00000002979	1 retrocopy	retro_lafr_632,
Mustela putorius furo	ENSMPUG00000016742	1 retrocopy	retro_mputfur_361,
Nomascus leucogenys	ENSNLEG00000001743	1 retrocopy	retro_nleu_1974,
Otolemur garnettii	ENSOGAG00000006358	1 retrocopy	retro_ogar_3442,
Pongo abelii	ENSPPYG00000004238	1 retrocopy	retro_pabe_3059,
Pan troglodytes	ENSPTRG00000023277	1 retrocopy	retro_ptro_2615,
Rattus norvegicus	ENSRNOG00000009236	1 retrocopy	retro_rnor_1806,
Ictidomys tridecemlineatus	ENSSTOG00000010153	2 retrocopies	retro_itri_1107, retro_itri_740,
Tursiops truncatus	ENSTTRG00000014260	1 retrocopy	retro_ttru_1035,