RetrogeneDB ID: retro_cfam_1195

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 26:18902074..18902790(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAF2
• Ensembl ID: ENSCAFG00000016684
• Aliases: None
• Description: None

Sequence

>retro_cfam_1195
ATGGCAGCGCCTGAGGAGCCGGATATAACCCAGGAGCAGACGGAGAAGCTGCTGCAGTTTCAGGATCTGACTGGCATAGC
ATCTATGGATCAATGCTGCCATCCCTTGGAACAGCATTACTGGGACATAGAGGCTGCTGTACAGGACCGATTGAATGAAC
AAGAGGGTGTGCCAGATGTTTTCAACCCACCTCCATCCTGACCCCTGCAAGTTAATACAGCTGAGCACAGGCCCTACAGT
TATGCTGTTGCAAGACCACAGCCAAGGGGGCTGCCTGGATGGGGTTATTACTTAATAATGCTTCCATTCCGATTTACCTA
CACAATACTTGATATATTTAGGTTTGCCCCTCGCAGCCGGGTCACTGACCCCGTTGGGGACATTGTTTCATTTATGTTCT
CTTTTGAAGAGAAATATGGGAGGGCACACCCTGCCTTCTACCAGGGAACGTACAGCCAGGCACTTAACGATGCCAACCGG
GAGCTTTGGTTGCTTTTGGTTTGTCTTCATGGAGATGATCCCCAGGACTCCGATGAGTTCTGTAGCAACACACTCTGGGC
CCTGAAGTTATTTCCCTAATAAACACTAGGATGCTTCTCTGGGCATGCTCCACAAATAAACCTGCGGGATATAGGGACTT
GCAGGCTTTAGGAGGGAACACCTATCCATTCCTGGCCTTGATTATGCTGAAGGATCAGAGAATGACTGCAGTGGGA

Alignment

ORF - retro_cfam_1195 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.44 %
• Parental protein coverage: 55.51 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAAPEERDLTQEQTEKLLQFQDLTGIESMDQCRHTLEQHNWNIEAAVQDRLNEQEGVPSVFNPPPSRPLQ
          MAAPEE.D.TQEQTEKLLQFQDLTGI.SMDQC.H.LEQH.W.IEAAVQDRLNEQEGVP.VFNPPPS.PLQ
Retrocopy MAAPEEPDITQEQTEKLLQFQDLTGIASMDQCCHPLEQHYWDIEAAVQDRLNEQEGVPDVFNPPPS*PLQ

Parental  VNTADHRIYSYVVSRPQPRGLLGWGYYLIMLPFRFTYYTILDIFRFALRFIRPDPRSRVTDPVGDIVSFM
          VNTA.HR.YSY.V.RPQPRGL.GWGYYLIMLPFRFT.YTILDIFRFA.R....DP...V.D.V....SF.
Retrocopy VNTAEHRPYSYAVARPQPRGLPGWGYYLIMLPFRFT-YTILDIFRFAPRSRVTDP---VGDIVSFMFSF-

Parental  HSFEEKYGRAHPVFYQGTYSQALNDAKRELRFLLVYLHGDDHQDSDEFCRNTLCA-PEVISLINTRMLFW
          ...EEKYGRAHP.FYQGTYSQALNDA.REL..LLV.LHGDD.QDSDEFC.NTL.A.PEVISLINTRML.W
Retrocopy ---EEKYGRAHPAFYQGTYSQALNDANRELWLLLVCLHGDDPQDSDEFCSNTLWA<PEVISLINTRMLLW

Parental  ACSTNKPEGYRVSQALRENTYPFLAMIMLKDRRMTVVG
          ACSTNKP.GYR..QAL..NTYPFLA.IMLKD.RMT.VG
Retrocopy ACSTNKPAGYRDLQALGGNTYPFLALIMLKDQRMTAVG

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	19.03 RPM
SRP017611_brain	0.00 RPM	13.18 RPM
SRP017611_kidney	0.00 RPM	16.77 RPM
SRP017611_liver	0.00 RPM	10.01 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1195 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1195 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1195 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000003903	1 retrocopy	retro_cfam_1797,
Canis familiaris	ENSCAFG00000016684	1 retrocopy	retro_cfam_1195 ,