RetrogeneDB ID: retro_cpor_969

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_37:17635030..17636289(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PAICS
• Ensembl ID: ENSCPOG00000010749
• Aliases: None
• Description: None

Sequence

>retro_cpor_969
GTATTGAACACTGGCAAAAAGCTCTATGAGGGTAAAACAAAAGAAGTCTATGGATTGTTGGATAGTCCAGGAGAAGTCCT
TCTGCAGTCCAAAGACCAGATTACAGCAGGAAATGCGGCCAGAAAGAATCACTTGGAAGGAAAAGCTGCAATCTCCAGTA
AGATTACCAGTTCTATTTTCGAGTTGTTACAGGAAGCAGGTATCAAGGCTGCTTTCACCAGAAAATGTGGGGAGACAGCT
TTCACTGCACCCCAGTGTGAAATGATTCCAATTGAATGGGTCTGCAGAAGAATAGCAGCTGGTTCTTTTCTCAAAAGAAA
TCCTGGTGTCAAGGAAGGATTTAAGTTTTACCCACCTAAAGTGGAGCTATTTTTTAAGGATGATGCTAATAATGATCCAC
AGTGGTCTGAAGAACAGCTAATTGCCGCAAAATTTTGCTTTGCTGGACTTGTTACAGGCCAAACTGAAGTGGATATCATG
AGTCATGCTACACAAGCTATTTTTGAAATACTGGAGAAATCCTGGTTGCCCCAGAACTGTATGCTGGTTGATATGAAGAT
TGGATGTGGTGTTGATGTGACCACCAAAGAAATTGTTCTCGCTGATGTTACTGACAATGATTCCTGGAGACTTTGGCCAT
CAGGAGATCGAAGCCAGCAGAAAGATAAAACAGTCTTACCGCGACCTCGCGGAAGTAACCCCTGGTGGGCTTCAGATGGT
AAAGAAAAACTTTGAGTGGGTTGCAGAGAGAGTAGAGCTTTTGAAATCAGAAGGTCAGTGCCGGGTTGTAGTTTTGATGG
GCTCAACTTCTGATGTTGGTCACTGTGAAAAAATCAAGAAGGCTTGTGGAAATTACGGAATTCCCTGTGAACTTCGAGTG
ACATCTGCCCATAAAGGCTCAGATGAAACTCTGATTAAAGCTGAATATGAAGGGGATGCCATTCTGACTGTGTTCGTGGC
AATAGCAGGCAGAAGCAATGTAAGTTTAGGCCCAGTGATGTCTGGTAACACTGCCAACCCAGTTATCAGCTGTCCTCAAC
CTCATATCCGCCTGGGGAGCTCGAGATGTGTGGTCTTCTCTGTGACTACCCAGGGGTCTCGGCTGTTCCATTATACTTTC
TCCAGAAGGATCAGCTCAGTTTGCAGCTCAGATTTTTGGATTAAACAACCACTTGGTATGGGCCAAACTGTGAGCAAACA
TATTGAACACATGGATTGCCTTGAAGCAGGCTAACAAGAAAATCAGAGAATGTAATTTC

Alignment

ORF - retro_cpor_969 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.02 %
• Parental protein coverage: 98.82 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VLKIGKKLYEGKTKEVYELLDSPGKVLLQSKDQITAGNAARKNHLEGKAAISNKITSCIFELLQEAGIKT
          VL..GKKLYEGKTKEVY.LLDSPG.VLLQSKDQITAGNAARKNHLEGKAAIS.KITS.IFELLQEAGIK.
Retrocopy VLNTGKKLYEGKTKEVYGLLDSPGEVLLQSKDQITAGNAARKNHLEGKAAISSKITSSIFELLQEAGIKA

Parental  AFTRKCGETAFIAPQCEMIPIEWVCRRIATGSFLKRNPGVKEGFKFYPPKVELFFKDDANNDPQWSEEQL
          AFTRKCGETAF.APQCEMIPIEWVCRRIA.GSFLKRNPGVKEGFKFYPPKVELFFKDDANNDPQWSEEQL
Retrocopy AFTRKCGETAFTAPQCEMIPIEWVCRRIAAGSFLKRNPGVKEGFKFYPPKVELFFKDDANNDPQWSEEQL

Parental  IAAKFCFAGLVIGQTEVDIMSHATQAIFEILEKSWLPQNCTLVDMKIEFGVDVTTKEIVLADVIDNDSWR
          IAAKFCFAGLV.GQTEVDIMSHATQAIFEILEKSWLPQNC.LVDMKI..GVDVTTKEIVLADV.DNDSWR
Retrocopy IAAKFCFAGLVTGQTEVDIMSHATQAIFEILEKSWLPQNCMLVDMKIGCGVDVTTKEIVLADVTDNDSWR

Parental  LWPSGDRSQQKD-KQSYRDLKEVTPEGLQMVKKNFEWVAERVELLLKSESQCRVVVLMGSTSDLGHCEKI
          LWPSGDRSQQKD.KQSYRDL.EVTP.GLQMVKKNFEWVAERVE.LLKSE.QCRVVVLMGSTSD.GHCEKI
Retrocopy LWPSGDRSQQKD>KQSYRDLAEVTPGGLQMVKKNFEWVAERVE-LLKSEGQCRVVVLMGSTSDVGHCEKI

Parental  KKACGNYGIPCELRVTSAHKGPDETLRIKAEYEGDGIPTVFVAVAGRSN-GLGPVMSGNTAYPVISCPP-
          KKACGNYGIPCELRVTSAHKG.DETL.IKAEYEGD.I.TVFVA.AGRSN..LGPVMSGNTA.PVISCP..
Retrocopy KKACGNYGIPCELRVTSAHKGSDETL-IKAEYEGDAILTVFVAIAGRSNVSLGPVMSGNTANPVISCPQ>

Parental  LTSDWGAQDVWSSLRLPSGLGCSTILSPEGSAQFAAQIFGLNNHLVWAKLRANILNTWIALKQADKKIRE
          L.S.WGA.DVWSSL.LP.GLGCS.ILSPEGSAQFAAQIFGLNNHLVWAKL.ANILNTWIALKQA.KKIRE
Retrocopy LISAWGARDVWSSL*LPRGLGCSIILSPEGSAQFAAQIFGLNNHLVWAKL*ANILNTWIALKQANKKIRE

Parental  CNF
          CNF
Retrocopy CNF

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	0.17 RPM	20.65 RPM
SRP017611_kidney	0.21 RPM	104.69 RPM
SRP017611_liver	0.17 RPM	35.52 RPM
SRP040447_lung	0.03 RPM	29.41 RPM
SRP040447_skeletal_muscle	0.04 RPM	27.03 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_969 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_969 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 15 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000010577	1 retrocopy	retro_btau_508,
Cavia porcellus	ENSCPOG00000010749	1 retrocopy	retro_cpor_969 ,
Dasypus novemcinctus	ENSDNOG00000013413	1 retrocopy	retro_dnov_284,
Echinops telfairi	ENSETEG00000015242	2 retrocopies	retro_etel_1918, retro_etel_341,
Homo sapiens	ENSG00000128050	3 retrocopies	retro_hsap_3802, retro_hsap_3915, retro_hsap_3927,
Gorilla gorilla	ENSGGOG00000024392	1 retrocopy	retro_ggor_2643,
Mus musculus	ENSMUSG00000029247	6 retrocopies	retro_mmus_1748, retro_mmus_2750, retro_mmus_2858, retro_mmus_3126, retro_mmus_653, retro_mmus_971,
Nomascus leucogenys	ENSNLEG00000008786	2 retrocopies	retro_nleu_1274, retro_nleu_2156,
Otolemur garnettii	ENSOGAG00000003575	2 retrocopies	retro_ogar_2138, retro_ogar_865,
Procavia capensis	ENSPCAG00000008531	1 retrocopy	retro_pcap_172,
Pan troglodytes	ENSPTRG00000016081	2 retrocopies	retro_ptro_2662, retro_ptro_2670,
Rattus norvegicus	ENSRNOG00000002101	3 retrocopies	retro_rnor_1891, retro_rnor_2768, retro_rnor_804,
Tupaia belangeri	ENSTBEG00000006751	1 retrocopy	retro_tbel_3697,
Tarsius syrichta	ENSTSYG00000010497	2 retrocopies	retro_tsyr_2170, retro_tsyr_329,
Drosophila melanogaster	FBgn0020513	1 retrocopy	retro_dmel_82,