RetrogeneDB ID: retro_cfam_1676

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 4:79981166..79981946(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AP5M1
• Ensembl ID: ENSCAFG00000015249
• Aliases: AP5M1, MUDENG
• Description: adaptor-related protein complex 5, mu 1 subunit [Source:HGNC Symbol;Acc:20192]

Sequence

>retro_cfam_1676
AATTTTGCTTTTGAGACACATCCATAAAAACATCCAGCCTAGAAATTTAGAACATTCAAAGAAAAACCACAGGTTTCTAT
TTCTATCACTGAAAAGGTAAAATCCATGCAACATGATAAATAGGATATAGCAGATACGTGGCAAATTGTCAGAACTATCA
CTTGCAAGTGTGATTTAGAAGGAATCATGCCAAATATTACCATCAGCTTGAGTCTCCCTACCAATGGATTTCCACTTGAG
AATATTCTAGTTCATCATTGTGTGACTTCTCTTGACTCTGCCATTCTAACTTTTAGTAGCACTGATGCAATGGATGCTTC
TGCATTTAGTGGACCTTACAAATTTCCATTCACTTCTCCTTTGAGTCATTCAACTTATGCTACTATACTTTCCAGGTCCC
TGTCCCTCCAATTGTGGATTTTTATCAAATGAAAGAGGAAGGAGTAAAAATAAAAATAACAGTTAATTTAAAACTTTATG
AACGTGTGAAAAATAATTTTGAATTCTGTGAAGCTCATATACCTTTTTTATAACAGAGGCCCGATTACATATGTGGAATG
CAAAGTTAGTTTTGGCCAGCTTGAAGTATTTTCAGAGAAAAGCTTATTGATCTGGGTTATTGGATAGAAGGTCCCCAAAT
TGATGGAAGTTAGTCTTTCTTGAACTATAACTTTTGGAGCCAAGAGTCACGGGAAGCAGCCATTTGACCAGATTTGCATT
GGAGGTACATATTTAAAACTTCATTTTAGAATCTTAGATTATATACTCAGCTCAAGTTTT

Alignment

ORF - retro_cfam_1676 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.85 %
• Parental protein coverage: 53.16 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NFASVTHPQKQPAWKVGTYKGKPQVSISITEKVKSMQYDKQDIADTWQVVGAVTCKCDLEGIMPNVTISL
          NFA..THP.K.PA.K..T.K.KPQVSISITEKVKSMQ.DK.DIADTWQ.V...TCKCDLEGIMPN.TISL
Retrocopy NFAFETHP*KHPA*KFRTFKEKPQVSISITEKVKSMQHDK*DIADTWQIVRTITCKCDLEGIMPNITISL

Parental  SLPTNGSPLQDILVHPCVTSLDSAILTSSSIDAMDDSAFSGPYKFPFTPPL-ESFNLCYYTSQVPVPPIL
          SLPTNG.PL..ILVH.CVTSLDSAILT.SS.DAMD.SAFSGPYKFPFT.PL.ESFNLCYYT.QVPVPPI.
Retrocopy SLPTNGFPLENILVHHCVTSLDSAILTFSSTDAMDASAFSGPYKFPFTSPL<ESFNLCYYTFQVPVPPIV

Parental  GFYQMKEEEIKVKITVNLKLHESVKNNFEFCEAHIP-FYNRGPITHVESKVSFGQLEVFREKSLLIWIIG
          .FYQMKEE..K.KITVNLKL.E.VKNNFEFCEAHIP.FYNRGPIT.VE.KVSFGQLEVF.EKSLLIW.IG
Retrocopy DFYQMKEEGVKIKITVNLKLYERVKNNFEFCEAHIP>FYNRGPITYVECKVSFGQLEVFSEKSLLIWVIG

Parental  QKFPKSMEISLSGTVTFGAKSHEKQPFDEICIGGTAYLKLHFKILDYTLTGCY
          .K.PK.ME.SLS.T.TFGAKSH.KQPFD.ICIGGT.YLKLHF.ILDY.L....
Retrocopy *KVPKLMEVSLS*TITFGAKSHGKQPFDQICIGGT-YLKLHFRILDYILSSSF

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	10.79 RPM
SRP017611_brain	0.00 RPM	9.37 RPM
SRP017611_kidney	0.00 RPM	16.38 RPM
SRP017611_liver	0.00 RPM	3.48 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1676 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1676 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1676 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002388	1 retrocopy	retro_amel_1700,
Canis familiaris	ENSCAFG00000015249	1 retrocopy	retro_cfam_1676 ,
Mustela putorius furo	ENSMPUG00000005943	1 retrocopy	retro_mputfur_210,
Nomascus leucogenys	ENSNLEG00000013007	1 retrocopy	retro_nleu_590,
Ictidomys tridecemlineatus	ENSSTOG00000011073	1 retrocopy	retro_itri_993,
Tupaia belangeri	ENSTBEG00000010976	1 retrocopy	retro_tbel_167,