RetrogeneDB ID: retro_cpor_5

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_3:61109943..61110996(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCPOG00000001179
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: TMEM185A
• Ensembl ID: ENSCPOG00000003622
• Aliases: None
• Description: None

Sequence

>retro_cpor_5
ATGAACCCCAGGGGGTTGTTCCAGGACTTCAACCCCAGTAAGTTCCTCATCTACGCCTGCCTTCTGCTTTTCTCCGTGTT
GCTGCCTCTGCGCTTGGACGGCGTCATCCAGTGGAGCTACTGGGCCGTGTTTGCCCCCATATGGCTATGGAAGCTCCTGG
TCGTCGCGGGGGCCTCGGTGGGTGCGGGCGTTTGGGCTCGCAACCCTCGCTACCGCACCGAGGGGGAGGCCGGCGTGGAG
TTCAAAGCCATGCTGATCGCCGTGGGCATCCACTTGCTGCTGCTCATGTTCGAAGTACTGGTCTGTGACCGGGTGGAGAG
GGGCACCCATTTCTGGCTGCTGGTCTTCATGCCTCTCTTCTTCGTCTCCCCCGTGTCTGTGGCCGCTTGTGTCTGGGGCT
TTCGACACGACAGGTCGCTGGAGCTGGAGATCCTGTGCTCCGTCAATATCCTGCAGTTCATCTTCATTGCCTTGAGGCTG
GACAGGATTATCCACTGGCCCTGGCTGGTGGTGTTCGTGCCGCTGTGGATCCTCATGTCCTTCCTTTGTCTGGTTGTCCT
CTATTACATCGTCTGGTCCCTCCTGTTTCTGAGGTCCCTGGACGTGGTCGCAGAGCAGCGAAGAACCCACGTGACCATGG
CCATCAGCTGGATAACGATTGTTGTGCCTCTGCTCACTTTTGAGGTCCTGCTGGTTCACAGATTGGATGGCCACAATACC
TTCTCTTACATCTCCATATTTGTCCCCCTTTGGCTGTCACTAGTAACTTTGATGGCCACAACTTTTAGGCGAAAAGGAGG
CAATCATTGGTGGTTTGGCATTCGCAGAGATTTCTGTCAGTTTCTGCTCGAAATTTTTCCATTTTTAAGAGAATATGGGA
ACATTTCCTATGATCTCCAACATGAAGATAGTGAAGACCCTGAAGAAACTGCCGGTCCAGAAGCTCCAAAAATCCCCCCA
ATGTTTGGAAAGAAGGCCAGGGTAGTTGTAACACAGAGCCCTGGAAAATACGTTCCCCCACCTCCTAAGTTAAATATTGA
TATGCCAGACTAG

Alignment

ORF - retro_cpor_5 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.68 %
• Parental protein coverage: 97.43 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FSPSKFLIYACLLLFSVLLALRLDGIIQWSYWAVFAPIWLWKLMVIVGASVGTGVWARNPQYRAEGETCV
          F.PSKFLIYACLLLFSVLL.LRLDG.IQWSYWAVFAPIWLWKL.V..GASVG.GVWARNP.YR.EGE..V
Retrocopy FNPSKFLIYACLLLFSVLLPLRLDGVIQWSYWAVFAPIWLWKLLVVAGASVGAGVWARNPRYRTEGEAGV

Parental  EFKAMLIAVGIHLLLLMFEVLVCDRIERGSHFWLLVFMPLFFVSPVSVAACVWGFRHDRSLELEILCSVN
          EFKAMLIAVGIHLLLLMFEVLVCDR.ERG.HFWLLVFMPLFFVSPVSVAACVWGFRHDRSLELEILCSVN
Retrocopy EFKAMLIAVGIHLLLLMFEVLVCDRVERGTHFWLLVFMPLFFVSPVSVAACVWGFRHDRSLELEILCSVN

Parental  ILQFIFIALRLDKIIHWPWLVVCVPLWILMSFLCLVVLYYIVWSVLFLRSMDVIAEQRRTHITMALSWMT
          ILQFIFIALRLD.IIHWPWLVV.VPLWILMSFLCLVVLYYIVWS.LFLRS.DV.AEQRRTH.TMA.SW.T
Retrocopy ILQFIFIALRLDRIIHWPWLVVFVPLWILMSFLCLVVLYYIVWSLLFLRSLDVVAEQRRTHVTMAISWIT

Parental  IVVPLLTFEILLVHKLDGHNAFSCIPIFVPLWLSLITLMATTFGQKGGNHWWFGIRKDFCQFLLEIFPFL
          IVVPLLTFE.LLVH.LDGHN.FS.I.IFVPLWLSL.TLMATTF..KGGNHWWFGIR.DFCQFLLEIFPFL
Retrocopy IVVPLLTFEVLLVHRLDGHNTFSYISIFVPLWLSLVTLMATTFRRKGGNHWWFGIRRDFCQFLLEIFPFL

Parental  REYGNISYDLHHEDNEETEETPVPEPPKIAPMFRKKARVVITQSPGKYVLPPPKLNIEMPD
          REYGNISYDL.HED.E..EET..PE.PKI.PMF.KKARVV.TQSPGKYV.PPPKLNI.MPD
Retrocopy REYGNISYDLQHEDSEDPEETAGPEAPKIPPMFGKKARVVVTQSPGKYVPPPPKLNIDMPD

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	11.27 RPM	9.49 RPM
SRP017611_kidney	11.20 RPM	8.90 RPM
SRP017611_liver	4.35 RPM	2.92 RPM
SRP040447_lung	17.38 RPM	10.06 RPM
SRP040447_skeletal_muscle	7.11 RPM	8.93 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_5 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_5 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 22 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000008637	1 retrocopy	retro_acar_65,
Ailuropoda melanoleuca	ENSAMEG00000009351	1 retrocopy	retro_amel_8,
Cavia porcellus	ENSCPOG00000003622	1 retrocopy	retro_cpor_5 ,
Dasypus novemcinctus	ENSDNOG00000011864	1 retrocopy	retro_dnov_2451,
Dipodomys ordii	ENSDORG00000015027	1 retrocopy	retro_dord_67,
Equus caballus	ENSECAG00000009399	1 retrocopy	retro_ecab_426,
Homo sapiens	ENSG00000155984	1 retrocopy	retro_hsap_104,
Gorilla gorilla	ENSGGOG00000024268	1 retrocopy	retro_ggor_189,
Loxodonta africana	ENSLAFG00000003044	1 retrocopy	retro_lafr_898,
Microcebus murinus	ENSMICG00000004639	1 retrocopy	retro_mmur_106,
Myotis lucifugus	ENSMLUG00000001319	1 retrocopy	retro_mluc_2075,
Macaca mulatta	ENSMMUG00000002888	1 retrocopy	retro_mmul_310,
Mustela putorius furo	ENSMPUG00000011896	1 retrocopy	retro_mputfur_46,
Mus musculus	ENSMUSG00000073139	1 retrocopy	retro_mmus_358,
Nomascus leucogenys	ENSNLEG00000013487	1 retrocopy	retro_nleu_2723,
Otolemur garnettii	ENSOGAG00000016414	1 retrocopy	retro_ogar_88,
Pongo abelii	ENSPPYG00000020809	1 retrocopy	retro_pabe_118,
Pteropus vampyrus	ENSPVAG00000013822	1 retrocopy	retro_pvam_30,
Rattus norvegicus	ENSRNOG00000011047	1 retrocopy	retro_rnor_6,
Sus scrofa	ENSSSCG00000012739	1 retrocopy	retro_sscr_494,
Ictidomys tridecemlineatus	ENSSTOG00000014484	1 retrocopy	retro_itri_8,
Tursiops truncatus	ENSTTRG00000000643	1 retrocopy	retro_ttru_868,