RetrogeneDB ID: retro_cpor_542

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_19:2654009..2654321(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SKA2
• Ensembl ID: ENSCPOG00000006051
• Aliases: None
• Description: spindle and kinetochore associated complex subunit 2 [Source:HGNC Symbol;Acc:28006]

Sequence

>retro_cpor_542
ACTGATCTGGATTATATTCAGTACAGGCTGGAATATGAAATCAAAACTAATTATCTTGATTCAGCTGGAGAGAAAAACCT
AGTAATACTCTTACAGGAATTGTCAGTGGTAAAATCTCAACAAGAAACGTTGCATGCATGTTTTAAACCCATTGCTATTG
AGCAGAAAGAGACTAAGAGCCACATTTATACTACTTTGGATACAACTATGACCATGATACAAGAATGATAAAAGCAAATA
GATGCAACACTATCGCCACTGACTGAAGAAGAAACAACTGTGACAGAGCAGTTAAAATCTCACACACCACAC

Alignment

ORF - retro_cpor_542 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.42 %
• Parental protein coverage: 85.95 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SDLDYIQYRLEYEIKTNHPDSAGEKNPVTLLKELSAIKSRYQTLCDHYKRVATEQKEIKTRISTTLNKTM
          .DLDYIQYRLEYEIKTN..DSAGEKN.V.LL.ELS..KS...TL....K..A.EQKE.K..I.TTL..TM
Retrocopy TDLDYIQYRLEYEIKTNYLDSAGEKNLVILLQELSVVKSQQETLHACFKPIAIEQKETKSHIYTTLDTTM

Parental  TRIQELQKLTDVELLPPTEEEKTATEQLKSHREH
          T.IQE..K..D..L.P.TEEE.T.TEQLKSH..H
Retrocopy TMIQE**KQIDATLSPLTEEETTVTEQLKSHTPH

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	3.39 RPM
SRP017611_kidney	0.00 RPM	1.88 RPM
SRP017611_liver	0.00 RPM	1.09 RPM
SRP040447_lung	0.00 RPM	2.75 RPM
SRP040447_skeletal_muscle	0.00 RPM	0.71 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_542 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_542 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 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021680	2 retrocopies	retro_btau_310, retro_btau_945,
Canis familiaris	ENSCAFG00000029233	1 retrocopy	retro_cfam_766,
Cavia porcellus	ENSCPOG00000006051	1 retrocopy	retro_cpor_542 ,
Dipodomys ordii	ENSDORG00000010768	2 retrocopies	retro_dord_103, retro_dord_281,
Equus caballus	ENSECAG00000015007	1 retrocopy	retro_ecab_987,
Felis catus	ENSFCAG00000022802	1 retrocopy	retro_fcat_1111,
Homo sapiens	ENSG00000182628	1 retrocopy	retro_hsap_4214,
Loxodonta africana	ENSLAFG00000003405	1 retrocopy	retro_lafr_1215,
Myotis lucifugus	ENSMLUG00000010942	1 retrocopy	retro_mluc_83,
Monodelphis domestica	ENSMODG00000014619	1 retrocopy	retro_mdom_347,
Mustela putorius furo	ENSMPUG00000015241	1 retrocopy	retro_mputfur_1435,
Mus musculus	ENSMUSG00000020492	2 retrocopies	retro_mmus_370, retro_mmus_778,
Otolemur garnettii	ENSOGAG00000026072	4 retrocopies	retro_ogar_1882, retro_ogar_2937, retro_ogar_3032, retro_ogar_907,
Rattus norvegicus	ENSRNOG00000025981	3 retrocopies	retro_rnor_1606, retro_rnor_523, retro_rnor_733,
Sorex araneus	ENSSARG00000011128	2 retrocopies	retro_sara_60, retro_sara_662,
Ictidomys tridecemlineatus	ENSSTOG00000024169	4 retrocopies	retro_itri_1115, retro_itri_1275, retro_itri_1434, retro_itri_725,
Tarsius syrichta	ENSTSYG00000006158	3 retrocopies	retro_tsyr_1620, retro_tsyr_2034, retro_tsyr_748,
Tursiops truncatus	ENSTTRG00000017196	1 retrocopy	retro_ttru_143,