RetrogeneDB ID: retro_cpor_1294

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_66:9587067..9587713(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZC3H15
• Ensembl ID: ENSCPOG00000012965
• Aliases: None
• Description: None

Sequence

>retro_cpor_1294
GTGCCCCCCAAGAAACAGGCTCAGGCGGGGGGCAGCAAAAAGGCGGAGCAAAAAAGAAGGAGAAGATTATTGAGGACAAA
ACTTTTGGTCTAAAGAACAAGAAAGGAGCAAAGCAACAGAAGTTTATCAAGGCTGTCACTCATCAAGTTAAATTTGGTCA
ACAAAATCCATGTCAGGTAGCACAAAGTGAAGCTGAAAAGAAATTGAAGAAAGATGACAAGAAGAAAGAATTGCAGGAGC
TAAATGAGCTCCTCAAACCTGTTGTCGCAGCTCAAAAAATAAGTAAAGGTGCAGACCCCAAGTCCGTGGTGTGTGCCTTC
TTCAAGCAGGGCCAGTGCAGGAAGGGTGACAAGTGCAAGTTTTCCCACGACCTGACTTTGGAGAGAAAATGTGAAAAACG
AAGTGTTTACATTGATGCAAGAGATGAAGAACTTGAAAAAGATACAATGGATAATTGGGATGAGAAACAGCTCGAAGAGG
TAGTGAACAAGAAGCACGGTGAGGCAGGAAAGAAAAAAACAAAAACTCAAATAGTCTGCAAGCATTCCTTGAAGCTATTG
AAAATAACAAGTATGGCTGGTTTTGGGTGTGCCCTGGAGGGGGTGATAATTGTATGTATCGGCATGCACTTCCTCCTGGA
TTTGTG

Alignment

ORF - retro_cpor_1294 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.04 %
• Parental protein coverage: 50.7 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MPPKKQAQAGGSKKAEQK-KKEKIIEDKTFGLKNKKGAKQQKFIKAVTHQVKFGQQNPRQVAQSEAEKKL
          .PPKKQAQAGGSKKAEQK.KKEKIIEDKTFGLKNKKGAKQQKFIKAVTHQVKFGQQNP.QVAQSEAEKKL
Retrocopy VPPKKQAQAGGSKKAEQK<KKEKIIEDKTFGLKNKKGAKQQKFIKAVTHQVKFGQQNPCQVAQSEAEKKL

Parental  KKDDKKKELQELNELFKPVVAAQKISKGADPKSVVCAFFKQGQCTKGDKCKFSHDLTLERKCEKRSVYID
          KKDDKKKELQELNEL.KPVVAAQKISKGADPKSVVCAFFKQGQC.KGDKCKFSHDLTLERKCEKRSVYID
Retrocopy KKDDKKKELQELNELLKPVVAAQKISKGADPKSVVCAFFKQGQCRKGDKCKFSHDLTLERKCEKRSVYID

Parental  ARDEELEKDTMDNWDEKKLEEVVNKKHGEAEKKKPKTQIVCKH-FLEAIENNKYGWFWVCPGGGDNCMYR
          ARDEELEKDTMDNWDEK.LEEVVNKKHGEA.K.....QIVCKH.FLEAIENNKYGWFWVCPGGGDNCMYR
Retrocopy ARDEELEKDTMDNWDEKQLEEVVNKKHGEAGKXXXXXQIVCKH<FLEAIENNKYGWFWVCPGGGDNCMYR

Parental  HALPPGFV
          HALPPGFV
Retrocopy HALPPGFV

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	0.06 RPM	52.40 RPM
SRP017611_kidney	0.10 RPM	48.68 RPM
SRP017611_liver	0.09 RPM	32.12 RPM
SRP040447_lung	0.08 RPM	31.95 RPM
SRP040447_skeletal_muscle	0.00 RPM	22.17 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1294 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1294 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 14 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021762	1 retrocopy	retro_btau_1223,
Choloepus hoffmanni	ENSCHOG00000011958	1 retrocopy	retro_chof_2120,
Callithrix jacchus	ENSCJAG00000005931	2 retrocopies	retro_cjac_2883, retro_cjac_3986,
Cavia porcellus	ENSCPOG00000012965	2 retrocopies	retro_cpor_1294 , retro_cpor_919,
Dipodomys ordii	ENSDORG00000011664	1 retrocopy	retro_dord_666,
Loxodonta africana	ENSLAFG00000001563	1 retrocopy	retro_lafr_941,
Myotis lucifugus	ENSMLUG00000007741	2 retrocopies	retro_mluc_1494, retro_mluc_2467,
Monodelphis domestica	ENSMODG00000027565	5 retrocopies	retro_mdom_1230, retro_mdom_1321, retro_mdom_1744, retro_mdom_1942, retro_mdom_871,
Oryctolagus cuniculus	ENSOCUG00000011903	1 retrocopy	retro_ocun_886,
Otolemur garnettii	ENSOGAG00000002182	2 retrocopies	retro_ogar_1093, retro_ogar_611,
Ochotona princeps	ENSOPRG00000015790	2 retrocopies	retro_opri_169, retro_opri_609,
Pan troglodytes	ENSPTRG00000012717	1 retrocopy	retro_ptro_348,
Rattus norvegicus	ENSRNOG00000005256	4 retrocopies	retro_rnor_2628, retro_rnor_284, retro_rnor_662, retro_rnor_925,
Sorex araneus	ENSSARG00000012071	1 retrocopy	retro_sara_363,