RetrogeneDB ID: retro_cfam_1462

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 32:6588224..6588588(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: OSTC
• Ensembl ID: ENSCAFG00000011286
• Aliases: None
• Description: Canis lupus familiaris oligosaccharyltransferase complex subunit (OSTC), mRNA. [Source:RefSeq mRNA;Acc:NM_001160121]

Sequence

>retro_cfam_1462
ATGATGGTGTATGCTCTCGTAGTGGTGGTATTACATCCTCCTCATCACAGGAGGAATAACTTATGATGTTATTGTTGAAC
CTCTGAATGTTGGCTCTATGACTGATGGACATGGACATCAGAGACCAGTAGTAGCTCTCTTGGCCCACAGAGTAAATGGA
TGATATACTATGAAAGGATTCACATCCAGCTCCCTATTTATAATGGGAGGTTTAGGTTTCTTAATCCTGGACTAATCAGA
TGTGCCAAACATTCCAAAACTCAATAGATTTCCTCTTCTATTCATTAGATTTGTCTGTGTCCTATTGAGTTTTTTCATAG
CTAGAGTATTCATGAAAATGGAACTGCGGGACTGTCTGATGGGT

Alignment

ORF - retro_cfam_1462 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.77 %
• Parental protein coverage: 79.87 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MTVYALV-VVSY-FLITGGIIYDVIVEPPSVGSMTDEHGHQRPV-AFLAYRVNGQYIMEGLASSFLFTMG
          M.VYALV.VV....LITGGI.YDVIVEP..VGSMTD.HGHQRPV.A.LA.RVNG.Y.M.G..SS.LF.MG
Retrocopy MMVYALVVVVLH>LLITGGITYDVIVEPLNVGSMTDGHGHQRPVVALLAHRVNG*YTMKGFTSSSLFIMG

Parental  GLGFIILDRSNAPNIPKLNRFLLLFIGFVCVLLSFFMARVFMRMKLPGYLMG
          GLGF.ILD.S..PNIPKLNRF.LLFI.FVCVLLSFF.ARVFM.M.L...LMG
Retrocopy GLGFLILD*SDVPNIPKLNRFPLLFIRFVCVLLSFFIARVFMKMELRDCLMG

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	0.04 RPM	7.06 RPM
SRP017611_brain	0.00 RPM	3.33 RPM
SRP017611_kidney	0.00 RPM	12.68 RPM
SRP017611_liver	0.00 RPM	2.47 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1462 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1462 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1462 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 44 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001753	2 retrocopies	retro_amel_1110, retro_amel_165,
Canis familiaris	ENSCAFG00000011286	12 retrocopies	retro_cfam_1129, retro_cfam_1206, retro_cfam_1459, retro_cfam_1462 , retro_cfam_1575, retro_cfam_1851, retro_cfam_1910, retro_cfam_1948, retro_cfam_2003, retro_cfam_263, retro_cfam_296, retro_cfam_814,
Callithrix jacchus	ENSCJAG00000016002	3 retrocopies	retro_cjac_121, retro_cjac_2981, retro_cjac_324,
Cavia porcellus	ENSCPOG00000024467	1 retrocopy	retro_cpor_659,
Echinops telfairi	ENSETEG00000003717	4 retrocopies	retro_etel_1564, retro_etel_492, retro_etel_878, retro_etel_970,
Gorilla gorilla	ENSGGOG00000026873	6 retrocopies	retro_ggor_1457, retro_ggor_2060, retro_ggor_215, retro_ggor_2427, retro_ggor_370, retro_ggor_385,
Monodelphis domestica	ENSMODG00000020599	1 retrocopy	retro_mdom_428,
Mustela putorius furo	ENSMPUG00000008869	1 retrocopy	retro_mputfur_1451,
Mus musculus	ENSMUSG00000041084	1 retrocopy	retro_mmus_648,
Oryctolagus cuniculus	ENSOCUG00000011056	2 retrocopies	retro_ocun_1318, retro_ocun_7,
Pteropus vampyrus	ENSPVAG00000005915	1 retrocopy	retro_pvam_924,
Rattus norvegicus	ENSRNOG00000023322	1 retrocopy	retro_rnor_2297,
Sus scrofa	ENSSSCG00000009145	1 retrocopy	retro_sscr_503,
Ictidomys tridecemlineatus	ENSSTOG00000021644	6 retrocopies	retro_itri_1211, retro_itri_1386, retro_itri_15, retro_itri_1571, retro_itri_789, retro_itri_863,
Tarsius syrichta	ENSTSYG00000000724	2 retrocopies	retro_tsyr_1193, retro_tsyr_921,