RetrogeneDB ID: retro_cfam_2208

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: X:107608022..107608478(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KIAA1143
• Ensembl ID: ENSCAFG00000014132
• Aliases: None
• Description: KIAA1143 [Source:HGNC Symbol;Acc:29198]

Sequence

>retro_cfam_2208
AACCAGGTTTCATACGTGGGGCCAGCTGAGCCGGCGTTCCTCTCCTGCTTCAAGGAATGTGTCGGCTTCAGGGAAGGGCC
CACCGTGGAAACCAAGAGAACCCAGCTTCAGCTCCCAGATGATGATGGTGATCACAGTGACAAAGAAGATGAACAGCAGC
CCCAAGTGGTGGTTTTAAAAAAGGGAGACCTGTCAGTTGAAGAAGTCATGAAAATTAAAGCAGAAATAAAAGCTGCGAAA
GCAGATGAAGAACCAGCTGCTGTTGATGGAAGAATCATTTATCAGAAACCAGTCAAGCGTTCATCAGATGAAAAATACTC
AGGTTTAACAGCAACTTGAAAAAAGAGGAAGGCAAAAGAAGATGAAATAAATAATCAGGACTCGGTTAAAAAGAACTCAC
AAAAGCAAATAAAAAACAGTTCCCTCCTTTCTTTTGACAATGAAGATGAACCTGCA

Alignment

ORF - retro_cfam_2208 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.11 %
• Parental protein coverage: 87.79 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NQVSYVRPAEPAFLARFKERVGYREGPTVETKRTQLQLPDEDGDHSDKEDE-QPQVVVLKKGDLSVEEVM
          NQVSYV.PAEPAFL..FKE.VG.REGPTVETKRTQLQLPD.DGDHSDKEDE.QPQVVVLKKGDLSVEEVM
Retrocopy NQVSYVGPAEPAFLSCFKECVGFREGPTVETKRTQLQLPDDDGDHSDKEDEQQPQVVVLKKGDLSVEEVM

Parental  KIKAEIKAAKADEEPAAVDGRIMYRKPVKRSSDEKYSGLTASSKKRKAKEDEINNQDSVKKNSQKQIKNS
          KIKAEIKAAKADEEPAAVDGRI.Y.KPVKRSSDEKYSGLTA..KKRKAKEDEINNQDSVKKNSQKQIKNS
Retrocopy KIKAEIKAAKADEEPAAVDGRIIYQKPVKRSSDEKYSGLTAT*KKRKAKEDEINNQDSVKKNSQKQIKNS

Parental  SLLSFDNEDEIA
          SLLSFDNEDE.A
Retrocopy SLLSFDNEDEPA

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	8.27 RPM
SRP017611_brain	0.00 RPM	3.49 RPM
SRP017611_kidney	0.00 RPM	9.71 RPM
SRP017611_liver	0.00 RPM	1.89 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_2208 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_2208 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_2208 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014132	1 retrocopy	retro_cfam_2208 ,
Homo sapiens	ENSG00000163807	2 retrocopies	retro_hsap_1399, retro_hsap_2762,
Nomascus leucogenys	ENSNLEG00000005987	1 retrocopy	retro_nleu_666,
Oryctolagus cuniculus	ENSOCUG00000000929	2 retrocopies	retro_ocun_1601, retro_ocun_432,
Pongo abelii	ENSPPYG00000013954	1 retrocopy	retro_pabe_2250,
Pan troglodytes	ENSPTRG00000014824	1 retrocopy	retro_ptro_1869,
Pteropus vampyrus	ENSPVAG00000012438	2 retrocopies	retro_pvam_367, retro_pvam_458,
Sus scrofa	ENSSSCG00000011308	2 retrocopies	retro_sscr_844, retro_sscr_874,
Ictidomys tridecemlineatus	ENSSTOG00000010817	1 retrocopy	retro_itri_307,