RetrogeneDB ID: retro_cpor_997

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_39:6042132..6042633(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BUB3
• Ensembl ID: ENSCPOG00000011957
• Aliases: None
• Description: None

Sequence

>retro_cpor_997
GTGTTAGTGCGCAACTTGCAGAACATGGGCTATGTGCAGCAGTGCAGGGAATCCAGCCTGAAATACCAGACTCATTGCAT
ACAAGCATTTCCAAATAAGCAGGGTTGAGTATTAAGCTCTATTGAAGGCCAAGTGGTAGTTGAATACTTGGACCCAAGCC
CTGAAGTGTACAAGAAAAAGTATGCCTGCAAATGTTACAGACTAAAAGAAAATAATATTGAGCAGATTTACCCAGTCAAT
GCCATTTCCTTTCACAATATCCACAATATGTTTGCCACAGATAGCTCTGATGGATTTGTAAATATTTGGGATCCATTTAA
TAAAAAGTAACTGAGCCAGTTTCATCGCTACCCCACCAGCATCGCCTCACTTGCCTACAGCAATGATGGGACTATGCCTG
CAATAGCATCATCATACATGTATGAAATGGATGACCCAGAACATCATGAAGATTATACCTTCATTCACCAAGTGATAGAT
ACAGAAACATAACCCAAGTCC

Alignment

ORF - retro_cpor_997 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.23 %
• Parental protein coverage: 50.91 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VLVWDLRNMGYVQQRRESSLKYQTRCIRAFPNKQGYVLSSIEGRVAVEYLDPSPEVQKKKYAFKCHRLKE
          VLV..L.NMGYVQQ.RESSLKYQT.CI.AFPNKQG.VLSSIEG.V.VEYLDPSPEV.KKKYA.KC.RLKE
Retrocopy VLVRNLQNMGYVQQCRESSLKYQTHCIQAFPNKQG*VLSSIEGQVVVEYLDPSPEVYKKKYACKCYRLKE

Parental  NNIEQIYPVNAISFHNIHNTFATGGSDGFVNIWDPFNKKRLCQFHRYPTSIASLAFSNDGTTLAIASSYM
          NNIEQIYPVNAISFHNIHN.FAT..SDGFVNIWDPFNKK.L.QFHRYPTSIASLA.SNDGT..AIASSYM
Retrocopy NNIEQIYPVNAISFHNIHNMFATDSSDGFVNIWDPFNKK*LSQFHRYPTSIASLAYSNDGTMPAIASSYM

Parental  YEMDDTEHPEDGIFIRQVTDAETKPKS
          YEMDD.EH.ED..FI.QV.D.ET.PKS
Retrocopy YEMDDPEHHEDYTFIHQVIDTET*PKS

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
SRP017611_brain	0.00 RPM	26.34 RPM
SRP017611_kidney	0.10 RPM	28.47 RPM
SRP017611_liver	0.00 RPM	18.06 RPM
SRP040447_lung	0.00 RPM	37.45 RPM
SRP040447_skeletal_muscle	0.00 RPM	20.99 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_997 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_997 was not experimentally validated.

Homology

Retrocopy orthology:

Cavia porcellus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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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,