RetrogeneDB ID: retro_cfam_835

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 18:53603331..53604033(-)
• Located in intron of: ENSCAFG00000025291

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZCCHC17
• Ensembl ID: ENSCAFG00000011131
• Aliases: None
• Description: zinc finger, CCHC domain containing 17 [Source:HGNC Symbol;Acc:30246]

Sequence

>retro_cfam_835
ATGAATTCAGGAAGACCCGAGACCATGGAGCACTTGCCTGCTCTCTACATTATTTTCCAAGGAGAGATTGCTATGGTTAC
AGACTATGGAGCCTTCATCAAAATCCCTGGCTGTCAGAAGCAAGGTCTGGTCCATCGAACTCACATGTCATCCTGTCGTA
TGGATAAGCCTTCTGAGATAGTGGATGATGGAGGCAAAGTATGGGTGAAGCTTATTGGCCGGGAGATGAAAAATGATAGG
ATAAAAGTATCCATATCCATGAAAGTCATCAACCAAGGAACTGGGAAAGACCTTGACCCCAACAACGTTATCATTGAGCA
AGAAGAGAGGCGGCTGCAGTCCTTCCAGGATTACACTGGGCAGAAGATCACCCTCGAGGCTGTCTTGAACACCACCTGCA
AGAAGTGTGGCTGCAAAGGCCACTTTGCAAAGGATTGTTTTATGCAACCAGGAGGGACCAAGTATTCTCTGATACCTGAT
GAGGAAGAGGAGAAGGAAGAGGCAAAGTCAGCAGAGTTTGAGAAGCCTGACTCCACAAGGAATTCTTCTAGAAAAAGAAA
GAAGGAAAAGAAGAAAAAAACCCATGGAGACAGGAAGTTGTCTGAGTCTGACAGCTCAGACTCTGAGAGTGACACAAGCA
AGAGGGCAAGGCACACATCAAAAGACAGCAAGGCAGCAAAGAAGAAGAAGCAGCACAGGGAA

Alignment

ORF - retro_cfam_835 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.75 %
• Parental protein coverage: 97.1 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNSGRPETMENLPALYTIFQGEVAMVTDYGAFIKIPGCRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVK
          MNSGRPETME.LPALY.IFQGE.AMVTDYGAFIKIPGC.KQGLVHRTHMSSCR.DKPSEIVD.G.KVWVK
Retrocopy MNSGRPETMEHLPALYIIFQGEIAMVTDYGAFIKIPGCQKQGLVHRTHMSSCRMDKPSEIVDDGGKVWVK

Parental  LIGREMKNDRIKVSLSMKVVNQGTGKDLDPNNVIIEQEERRRRSFQDYTGQKITLEAVLNTTCKKCGCKG
          LIGREMKNDRIKVS.SMKV.NQGTGKDLDPNNVIIEQEERR..SFQDYTGQKITLEAVLNTTCKKCGCKG
Retrocopy LIGREMKNDRIKVSISMKVINQGTGKDLDPNNVIIEQEERRLQSFQDYTGQKITLEAVLNTTCKKCGCKG

Parental  HFAKDCFMQPGGTKYSLIPDEEEEKEEAKSAEFEKPDPTRNSSRKRKKEKKKKKHRDRKSSDSDSSDSES
          HFAKDCFMQPGGTKYSLIPDEEEEKEEAKSAEFEKPD.TRNSS...........H.DRK.S.SDSSDSES
Retrocopy HFAKDCFMQPGGTKYSLIPDEEEEKEEAKSAEFEKPDSTRNSSXXXXXXXXXXXHGDRKLSESDSSDSES

Parental  DTGKRARHTSKDSKAAKKKKKKKK
          DT.KRARHTSKDSKAAKKKK....
Retrocopy DTSKRARHTSKDSKAAKKKKQHRE

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	21.29 RPM
SRP017611_brain	0.24 RPM	31.60 RPM
SRP017611_kidney	3.96 RPM	10.96 RPM
SRP017611_liver	1.09 RPM	4.71 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_835 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_835 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_835 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017710	1 retrocopy	retro_amel_1501,
Bos taurus	ENSBTAG00000016818	2 retrocopies	retro_btau_168, retro_btau_273,
Canis familiaris	ENSCAFG00000011131	2 retrocopies	retro_cfam_485, retro_cfam_835 ,
Callithrix jacchus	ENSCJAG00000006259	1 retrocopy	retro_cjac_4218,
Dasypus novemcinctus	ENSDNOG00000000509	1 retrocopy	retro_dnov_2548,
Dipodomys ordii	ENSDORG00000004128	1 retrocopy	retro_dord_200,
Echinops telfairi	ENSETEG00000007421	1 retrocopy	retro_etel_1280,
Loxodonta africana	ENSLAFG00000015364	1 retrocopy	retro_lafr_534,
Myotis lucifugus	ENSMLUG00000000594	1 retrocopy	retro_mluc_2176,
Monodelphis domestica	ENSMODG00000017082	1 retrocopy	retro_mdom_252,
Mustela putorius furo	ENSMPUG00000015442	1 retrocopy	retro_mputfur_680,
Mus musculus	ENSMUSG00000028772	1 retrocopy	retro_mmus_2150,
Otolemur garnettii	ENSOGAG00000013749	1 retrocopy	retro_ogar_1225,
Sorex araneus	ENSSARG00000007944	1 retrocopy	retro_sara_691,
Ictidomys tridecemlineatus	ENSSTOG00000003825	1 retrocopy	retro_itri_405,
Tursiops truncatus	ENSTTRG00000014870	2 retrocopies	retro_ttru_1383, retro_ttru_1613,