RetrogeneDB ID: retro_cfam_433

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 11:60600293..60600723(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KCTD5
• Ensembl ID: ENSCAFG00000019357
• Aliases: None
• Description: potassium channel tetramerization domain containing 5 [Source:HGNC Symbol;Acc:21423]

Sequence

>retro_cfam_433
GGGCTCGGTGCCCTGGCCCAGGACCCCCGCCGCGTGTCCAAGTGGGTCCGGCTCAACGTTGGCGGCACCTACCTCCTCAC
CACCTGGCAGACCCCCTGCCGGGACCCGAAATCCTTCCGTCCTGTCTGTGCCAGGCCAACCCCGACCTGGACTCAGACAA
GGATGAAACTGGTGCCCATTTAGTCGACAGAGACCCCTACTTTGGGCCTGCGCTGAACTACCTGAGCTCAGGAAGCGGGT
CATTAACAAAGATCTCGCAGAGGAAGGAGTGTTGGAGGGAAGGGAATTTTACAATATCACCTCACTAATAAAACTTGTAA
AGGACAAAATTCCAGAACGAGACAGCAAAACCTCCCAGGTGCCGGTGAAGCACGTATACCATGTGCTGCAGCGACAGGTG
GAGGAGCTCACCCAGATGGTGTCCACCATC

Alignment

ORF - retro_cfam_433 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.27 %
• Parental protein coverage: 61.97 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GLGALAQRPGGVSKWVRLNVGGTYFLTTRQTLCRD-PKSFLYRLCQADPDLDSDKDETGAYLIDRDPTYF
          GLGALAQ.P..VSKWVRLNVGGTY.LTT.QT.CRD.P......LCQA.PDLDSDKDETGA.L.DRDP.YF
Retrocopy GLGALAQDPRRVSKWVRLNVGGTYLLTTWQTPCRD<PEILPSCLCQANPDLDSDKDETGAHLVDRDP-YF

Parental  GPVLNYLRHG-KLVINKDLAEEGVLEEAEFYNITSLIKLVKDKIRERDSKTSQVPVKHVYRVLQCQEEEL
          GP.LNYL..G.K.VINKDLAEEGVLE..EFYNITSLIKLVKDKI.ERDSKTSQVPVKHVY.VLQ.Q.EEL
Retrocopy GPALNYLSSG<KRVINKDLAEEGVLEGREFYNITSLIKLVKDKIPERDSKTSQVPVKHVYHVLQRQVEEL

Parental  TQMVSTM
          TQMVST.
Retrocopy TQMVSTI

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	13.69 RPM
SRP017611_brain	0.00 RPM	3.02 RPM
SRP017611_kidney	0.00 RPM	5.61 RPM
SRP017611_liver	0.00 RPM	3.05 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_433 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_433 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_433 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000019357	1 retrocopy	retro_cfam_433 ,
Homo sapiens	ENSG00000167977	1 retrocopy	retro_hsap_2224,
Gorilla gorilla	ENSGGOG00000010496	1 retrocopy	retro_ggor_1752,
Monodelphis domestica	ENSMODG00000016596	1 retrocopy	retro_mdom_506,
Sarcophilus harrisii	ENSSHAG00000006867	1 retrocopy	retro_shar_158,
Ictidomys tridecemlineatus	ENSSTOG00000006647	8 retrocopies	retro_itri_1562, retro_itri_1690, retro_itri_1692, retro_itri_1761, retro_itri_1779, retro_itri_1844, retro_itri_1889, retro_itri_950,
Tursiops truncatus	ENSTTRG00000008237	1 retrocopy	retro_ttru_1510,