RetrogeneDB ID: retro_cfam_399

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 10:61496560..61497067(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000029900
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: BUB3
• Ensembl ID: ENSCAFG00000012700
• Aliases: None
• Description: BUB3 mitotic checkpoint protein [Source:HGNC Symbol;Acc:1151]

Sequence

>retro_cfam_399
GTCTTGGTGTGGGACTTACGGAACATGGGCAATGTGCAGCAGTGCCGCGAGTCCAGACTGAAGTACCAGACTCGCTGCAT
ACGAGCATTTCCAAACAAGCAGGGTTATGTATTAAGCTCTATCAAGGGCCGAGTGGCATTTGAGTACTTGGACCCAAGCC
CTGAGGAACAGAAGAAGCATGCCTTCAAGTGTCACAGACTAAAGGGGAACAGTATTGAGCAGATTTACCCTGTCAATGCC
ATTTCCTTTCACAACATCCACGATATGTTTGCCACAGGTGGCTCTGATGGATCTGTAAACATTTGGGATCCATTTAACAA
AAAGCGACTGTGCCAGTTCTATCAGTACCCCACCAGCATTGCGTCCCTTGCCTTCAGTAATGATGGGACCACGCTCGCAA
TAGCATCGTCGTATATGTATGAAATGGATGACATGGAACATCCTGAAGATGGAATTTTCATTTGCCAAGTGACAGACGCA
GAAACAAAACCCAAGTCACCATGTACT

Alignment

ORF - retro_cfam_399 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90. %
• Parental protein coverage: 68.55 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VLVWDLRNMGYVQQRRESSLKYQTRCIRAFPNKQGYVLSSIEGRVAVEYLDPSPEVQKKKYAFKCHRLKE
          VLVWDLRNMG.VQQ.RES.LKYQTRCIRAFPNKQGYVLSSI.GRVA.EYLDPSPE.QKK..AFKCHRLK.
Retrocopy VLVWDLRNMGNVQQCRESRLKYQTRCIRAFPNKQGYVLSSIKGRVAFEYLDPSPEEQKK-HAFKCHRLKG

Parental  NNIEQIYPVNAISFHNIHNTFATGGSDGFVNIWDPFNKKRLCQFHRYPTSIASLAFSNDGTTLAIASSYM
          N.IEQIYPVNAISFHNIH..FATGGSDG.VNIWDPFNKKRLCQF..YPTSIASLAFSNDGTTLAIASSYM
Retrocopy NSIEQIYPVNAISFHNIHDMFATGGSDGSVNIWDPFNKKRLCQFYQYPTSIASLAFSNDGTTLAIASSYM

Parental  YEMDDTEHPEDGIFIRQVTDAETKPKSPCT
          YEMDD.EHPEDGIFI.QVTDAETKPKSPCT
Retrocopy YEMDDMEHPEDGIFICQVTDAETKPKSPCT

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	0.04 RPM	55.56 RPM
SRP017611_brain	0.08 RPM	30.01 RPM
SRP017611_kidney	0.00 RPM	53.95 RPM
SRP017611_liver	0.00 RPM	17.84 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_399 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_399 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_399 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000012700	1 retrocopy	retro_cfam_399 ,
Callithrix jacchus	ENSCJAG00000001066	1 retrocopy	retro_cjac_3085,
Cavia porcellus	ENSCPOG00000011957	1 retrocopy	retro_cpor_997,
Homo sapiens	ENSG00000154473	1 retrocopy	retro_hsap_3887,
Gorilla gorilla	ENSGGOG00000023971	1 retrocopy	retro_ggor_2614,
Myotis lucifugus	ENSMLUG00000017732	1 retrocopy	retro_mluc_627,
Macaca mulatta	ENSMMUG00000003092	1 retrocopy	retro_mmul_1729,
Nomascus leucogenys	ENSNLEG00000027075	1 retrocopy	retro_nleu_1887,
Procavia capensis	ENSPCAG00000007736	1 retrocopy	retro_pcap_412,
Pongo abelii	ENSPPYG00000002731	1 retrocopy	retro_pabe_3168,
Ictidomys tridecemlineatus	ENSSTOG00000021785	1 retrocopy	retro_itri_1095,
Tarsius syrichta	ENSTSYG00000013444	2 retrocopies	retro_tsyr_1652, retro_tsyr_732,
Tursiops truncatus	ENSTTRG00000016194	1 retrocopy	retro_ttru_1136,