RetrogeneDB ID: retro_cfam_1792

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 6:41143301..41144042(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MED4
• Ensembl ID: ENSCAFG00000004451
• Aliases: None
• Description: mediator complex subunit 4 [Source:HGNC Symbol;Acc:17903]

Sequence

>retro_cfam_1792
AACAGCACGCGGGAGCGGCTGCTGTCTGCGCTGGAGGACCTGGAGGTCTTGTCGAGAGAACTTATAGAAATGCTGGCAAT
TTCAAGAAACCAAAAGTTGTTGCCGCCTGATGAGGAAAACCAGGTCCTGGAGTTGTTAATTCATAGAGATGGGGAATTTC
AAGAACTGATGAAGTTGGCACTTAATCAGGGAAAAATCCATCATGAAATGCACGTTTTAGAAAAGGAAGTGGAGAAGAGG
GACAGTGATATTCAGCAACTACAGAAACAGCTAAAGGAAGCAGAGCAAATACTGGCAACAGCTGTTTACCAAGCAAAAGA
AAAACTCAAATCAATAGAAAAGGCAAGAAAAGGTGCCATCTCCTCTGAAGAAATAATTAAATATGCACATAGAATAAGTG
CAAGTAATGCTGTGTGTGCTCCACTGACCTGGGTTCCAGGGGACCCACGGAGACCATACCCAACTGATTTAGAGATGAGA
AGTGGATTATTGGGTCAAATGAACAATCCTTCCACGAATGGTGTAAATGGTCATTTACCAGGGGATGCACTTGCAGCAGG
CAGATTGCCAGATGTCCTTGCCTCGCAGTACCCATGGCAGTCAAATGACATGTCAATGAATATGTTACCACCAAATCACA
GTAATGACTTCTTGTTGGAACCTCCGGGGCATAATAAAGAAAATGAAGATGATGTAGAAGTTATGTCAACAGACTCCTCG
AGCAGTAGCAGTGACTCTGAT

Alignment

ORF - retro_cfam_1792 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.19 %
• Parental protein coverage: 91.14 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NSTRERLLSALEDLEVLSRELIEMLAISRNQKLLPPDEENQVLELLIHRDGEFQELMKLALNQGKIHHEM
          NSTRERLLSALEDLEVLSRELIEMLAISRNQKLLPPDEENQVLELLIHRDGEFQELMKLALNQGKIHHEM
Retrocopy NSTRERLLSALEDLEVLSRELIEMLAISRNQKLLPPDEENQVLELLIHRDGEFQELMKLALNQGKIHHEM

Parental  QVLEKEVEKRDSDIQQLQKQLKEAEQILATAVYQAKEKLKSIEKARKGAISSEEIIKYAHRISASNAVCA
          .VLEKEVEKRDSDIQQLQKQLKEAEQILATAVYQAKEKLKSIEKARKGAISSEEIIKYAHRISASNAVCA
Retrocopy HVLEKEVEKRDSDIQQLQKQLKEAEQILATAVYQAKEKLKSIEKARKGAISSEEIIKYAHRISASNAVCA

Parental  PLTWVPGDPRRPYPTDLEMRSGLLGQMNNPSTNGVNGHLPGDALAAGRLPDVLAPQYPWQSNDMSMNMLP
          PLTWVPGDPRRPYPTDLEMRSGLLGQMNNPSTNGVNGHLPGDALAAGRLPDVLA.QYPWQSNDMSMNMLP
Retrocopy PLTWVPGDPRRPYPTDLEMRSGLLGQMNNPSTNGVNGHLPGDALAAGRLPDVLASQYPWQSNDMSMNMLP

Parental  PNHSNDFLLEPPGHNKENEDDVEVMSTDSSSSSSDSD
          PNHSNDFLLEPPGHNKENEDDVEVMSTDSSSSSSDSD
Retrocopy PNHSNDFLLEPPGHNKENEDDVEVMSTDSSSSSSDSD

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	7.06 RPM
SRP017611_brain	0.00 RPM	6.59 RPM
SRP017611_kidney	0.00 RPM	7.73 RPM
SRP017611_liver	0.00 RPM	2.83 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1792 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1792 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1792 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 9 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003718	1 retrocopy	retro_amel_1882,
Canis familiaris	ENSCAFG00000004451	1 retrocopy	retro_cfam_1792 ,
Callithrix jacchus	ENSCJAG00000009256	1 retrocopy	retro_cjac_3937,
Dasypus novemcinctus	ENSDNOG00000018064	1 retrocopy	retro_dnov_1342,
Myotis lucifugus	ENSMLUG00000009265	1 retrocopy	retro_mluc_178,
Mustela putorius furo	ENSMPUG00000001437	1 retrocopy	retro_mputfur_162,
Mus musculus	ENSMUSG00000022109	1 retrocopy	retro_mmus_3576,
Sorex araneus	ENSSARG00000001473	1 retrocopy	retro_sara_353,
Tupaia belangeri	ENSTBEG00000014259	1 retrocopy	retro_tbel_292,