RetrogeneDB ID: retro_cfam_726

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 16:20141879..20142769(-)
• Located in intron of: ENSCAFG00000032520

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000000713
• Aliases: EMC2, TTC35
• Description: None

Sequence

>retro_cfam_726
ATGGCGAAGGTCTCAGAGCTTTACGATGTCACTTGGGAAGAAATGCGAGATAAAATGAGAAAATGGAGAGAGAAAACTCA
CGAAACAGTGAGCAAATTGTGGAAGTTGGAGAGGAATTAATTAATGAATATGCTTCTAAGCTTGGAGATGATATTTGGAT
CATATATGAACAAGTGATGATTGCAGCCCTAGACTATGGTCGAGATGACTTGGCATTGTTTTGTCTTCAGGAGTTGAGAA
GACAGTTTCCTGGCAGCCACAGAGTCAAGAGACTAACAGGCATGAGATTTGAAGCCATGGAAAGATATGATGATGCTATA
CAACTATATGATCGAATTTGACAAGAAGATCCAACTAACACTGCTGCAAGAAAGCGTAAGATTGCCATTCGAAAAGCCCA
GGGGAAAAATGTGGAGGCCATTCGGGAACTGAATGAGTATCTGGAACAATTTGTTGGGGACCAAGAAGCCTGGCATGAAC
TTGCAGAACTTTATATCAATGAACACGACTATGCTAAAGCAGCCTTTTGTTTAGAGGAGCTAATGATGACTAATCCACAC
AACCACTTATACTGTCAGCAGTATGCTGAAGTTAAATATACCCAGGGTGCACTTGAAAACCTCGAACTTTCAAGAAAGTA
TTTTGCACAGGCACTGAAACTGAACAACAGAAATATGAGAGCTTTGTTTGGGCTTTACATGTCAGCAAGTCATATTGCTT
CTAATCCAAAAGCAAGTGCAAAAACAAAAAAGGACAACATGAAATATGCTAGTTGGGCAGCTAGTCAAATAAACAGAGCT
TATCAGTTTGCAGGTCGAAGTAAGAAGGAAGCTAAATACTCTCTTGAGGCAGTTGAAGACATGTTGGAAACACTGCAGAT
CACCCAGTCT

Alignment

ORF - retro_cfam_726 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.32 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAKVSELYDVTWEEMRDKMRKWRE-ENSRNSEQIVEVGEELINEYASKLGDDIWIIYEQVMIAALDYGRD
          MAKVSELYDVTWEEMRDKMRKWRE.ENSRNSEQIVEVGEELINEYASKLGDDIWIIYEQVMIAALDYGRD
Retrocopy MAKVSELYDVTWEEMRDKMRKWRE<ENSRNSEQIVEVGEELINEYASKLGDDIWIIYEQVMIAALDYGRD

Parental  DLALFCLQELRRQFPGSHRVKRLTGMRFEAMERYDDAIQLYDRILQEDPTNTAARKRKIAIRKAQGKNVE
          DLALFCLQELRRQFPGSHRVKRLTGMRFEAMERYDDAIQLYDRI.QEDPTNTAARKRKIAIRKAQGKNVE
Retrocopy DLALFCLQELRRQFPGSHRVKRLTGMRFEAMERYDDAIQLYDRI*QEDPTNTAARKRKIAIRKAQGKNVE

Parental  AIRELNEYLEQFVGDQEAWHELAELYINEHDYAKAAFCLEELMMTNPHNHLYCQQYAEVKYTQGGLENLE
          AIRELNEYLEQFVGDQEAWHELAELYINEHDYAKAAFCLEELMMTNPHNHLYCQQYAEVKYTQG.LENLE
Retrocopy AIRELNEYLEQFVGDQEAWHELAELYINEHDYAKAAFCLEELMMTNPHNHLYCQQYAEVKYTQGALENLE

Parental  LSRKYFAQALKLNNRNMRALFGLYMSASHIASNPKASAKTKKDNMKYASWAASQINRAYQFAGRSKKETK
          LSRKYFAQALKLNNRNMRALFGLYMSASHIASNPKASAKTKKDNMKYASWAASQINRAYQFAGRSKKE.K
Retrocopy LSRKYFAQALKLNNRNMRALFGLYMSASHIASNPKASAKTKKDNMKYASWAASQINRAYQFAGRSKKEAK

Parental  YSLKAVEDMLETLQITQS
          YSL.AVEDMLETLQITQS
Retrocopy YSLEAVEDMLETLQITQS

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	0.34 RPM	20.08 RPM
SRP017611_brain	0.16 RPM	14.93 RPM
SRP017611_kidney	0.13 RPM	22.45 RPM
SRP017611_liver	0.00 RPM	6.45 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_726 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_726 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_726 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 10 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012826	1 retrocopy	retro_amel_600,
Canis familiaris	ENSCAFG00000000713	1 retrocopy	retro_cfam_726 ,
Choloepus hoffmanni	ENSCHOG00000011271	3 retrocopies	retro_chof_1512, retro_chof_1990, retro_chof_851,
Callithrix jacchus	ENSCJAG00000006437	2 retrocopies	retro_cjac_3295, retro_cjac_3867,
Dasypus novemcinctus	ENSDNOG00000013708	1 retrocopy	retro_dnov_568,
Myotis lucifugus	ENSMLUG00000013258	2 retrocopies	retro_mluc_2369, retro_mluc_2452,
Mustela putorius furo	ENSMPUG00000005915	1 retrocopy	retro_mputfur_1647,
Mus musculus	ENSMUSG00000022337	1 retrocopy	retro_mmus_1262,
Oryctolagus cuniculus	ENSOCUG00000002461	1 retrocopy	retro_ocun_1251,
Pongo abelii	ENSPPYG00000018820	1 retrocopy	retro_pabe_1600,