RetrogeneDB ID: retro_cpor_893

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_32:14165083..14165599(+)
• Located in intron of: ENSCPOG00000000149

Retrocopy information

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

Parental gene information

• Parental gene symbol: TIMM17B
• Ensembl ID: ENSCPOG00000008768
• Aliases: None
• Description: None

Sequence

>retro_cpor_893
ATGGAGAACTATGCTGGAGAGCCTTGCCCATGGCGAATTGTGGAGGACTGCAGTGAATCTTTCATGGTAGGCATGATCAG
TGATGGGGTCTTCCAAACTATCAAGGGCTTCCACAATGCTCCCGTTAGAATTCAATATTGACTGAGCAGCAGTGTTAATA
CTGCAAGGATCAAAGCACCCCAGATTGGAGATAGCTTCATAGTGTGTGGGGAGCCTGTTTGTCACCATTGACTGTGCCCT
AGTGCGAATGCAGAGTAAGGAGAACCCTTGGAACTCCATCACCAGCAGAGCCCTAACAGGGTCTGTGCTGGCTGCCTGCA
GTGGTCCACAAGCCATAGTGGGCTCTGTGATGATGGGGGTTATCCTGCTGGCCATCATTGAGGACATCAGCATCCTCTTC
ATTTGTTACACTGCCCAGCAGTTCCACAACACAGCCCGATTCCTGGAGGATGCAGGCCAGCTGCCCCCTAACGCAGGGTA
CCAGCCCCAGGCTATCCCAGCTATCAGCGTTACCAT

Alignment

ORF - retro_cpor_893 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.24 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MEEYAREPCPWRIVDDCGGAFTMGVIGGGVFQAIKGFRNAPVGIQHRLRGSVNAVRIRAPQIGGSFAVWG
          ME.YA.EPCPWRIV.DC...F..G.I..GVFQ.IKGF.NAPV.IQ..L..SVN..RI.APQIG.SF.V.G
Retrocopy MENYAGEPCPWRIVEDCSESFMVGMISDGVFQTIKGFHNAPVRIQY*LSSSVNTARIKAPQIGDSFIVCG

Parental  -GLFSTIDCGLVRMRGKEDPWNSITSGALTGAVLAARSGPLAMVGSAMMGGILLALIEGVGILLTRYTAQ
          ..LF.TIDC.LVRM..KE.PWNSITS.ALTG.VLAA.SGP.A.VGS.MMG.ILLA.IE...IL...YTAQ
Retrocopy >SLFVTIDCALVRMQSKENPWNSITSRALTGSVLAACSGPQAIVGSVMMGVILLAIIEDISILFICYTAQ

Parental  QFRNAPPFLEDPSQLPPKEG-TPAPGYSSYQQYH
          QF.N...FLED..QLPP..G..PAPGY.SYQ.YH
Retrocopy QFHNTARFLEDAGQLPPNAG<VPAPGYPSYQRYH

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	7.07 RPM
SRP017611_kidney	0.00 RPM	21.57 RPM
SRP017611_liver	0.00 RPM	18.19 RPM
SRP040447_lung	0.05 RPM	21.26 RPM
SRP040447_skeletal_muscle	0.00 RPM	23.04 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_893 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_893 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 18 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012474	1 retrocopy	retro_amel_717,
Bos taurus	ENSBTAG00000018496	4 retrocopies	retro_btau_1022, retro_btau_1550, retro_btau_1552, retro_btau_882,
Cavia porcellus	ENSCPOG00000008768	2 retrocopies	retro_cpor_867, retro_cpor_893 ,
Dasypus novemcinctus	ENSDNOG00000025897	2 retrocopies	retro_dnov_2282, retro_dnov_2406,
Felis catus	ENSFCAG00000002569	2 retrocopies	retro_fcat_1429, retro_fcat_1654,
Gorilla gorilla	ENSGGOG00000011427	1 retrocopy	retro_ggor_779,
Macropus eugenii	ENSMEUG00000004174	1 retrocopy	retro_meug_2071,
Microcebus murinus	ENSMICG00000005971	3 retrocopies	retro_mmur_1128, retro_mmur_1272, retro_mmur_232,
Myotis lucifugus	ENSMLUG00000009148	1 retrocopy	retro_mluc_148,
Macaca mulatta	ENSMMUG00000004547	1 retrocopy	retro_mmul_796,
Mustela putorius furo	ENSMPUG00000013675	1 retrocopy	retro_mputfur_1232,
Mus musculus	ENSMUSG00000031158	1 retrocopy	retro_mmus_1509,
Nomascus leucogenys	ENSNLEG00000007902	1 retrocopy	retro_nleu_1616,
Oryctolagus cuniculus	ENSOCUG00000027418	2 retrocopies	retro_ocun_121, retro_ocun_1451,
Pteropus vampyrus	ENSPVAG00000007643	1 retrocopy	retro_pvam_470,
Ictidomys tridecemlineatus	ENSSTOG00000014173	1 retrocopy	retro_itri_83,
Tarsius syrichta	ENSTSYG00000010396	2 retrocopies	retro_tsyr_1132, retro_tsyr_1703,
Vicugna pacos	ENSVPAG00000009578	1 retrocopy	retro_vpac_92,