RetrogeneDB ID: retro_cpor_1237

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_6:18426665..18427278(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: STARD3NL
• Ensembl ID: ENSCPOG00000004394
• Aliases: None
• Description: None

Sequence

>retro_cpor_1237
CATCAACCCCACGCGGCACATAGCCAGGACCGAGTCCTACAAGAGAAGGGAGAAGAAAGACGTATCAGGAGGACCTTCTG
TTTGCTAGTCACCTTTGACCTCTGATTTGTAATATTACTGCAGGTAATAGAGTTGCATGTGAAGAGGAGCACTGAGAACA
CATTGGAGAAACAGGTGGTGTGGTAGGATTACTGCTCTTATTTTAATATATTTCTCTTGGCAGTTTCCCGTTTTAAAGTG
CGGATCCTTGCACATTCTGTGCGCAGACTGCGCCACTCATGGGCAAAAGCCTTGATGACAGCAGTGACCAGGGCCTTTCT
ACTAGGGAAAGTGGTCCTCTCAAAGCTTTCCTCACAGGGGATGTTTGGCTAAGTGCTGCCCATCATTTCATTCATCCTTG
CCTGACTTGAAACTTGGTTTCTAGATTTCAAAGTGTTACCTAAAGAAGCAGAAGAGGGAAACAGACTCCTTAGTGCTCAG
GATGCGTCGGAGAGGGCTGCCCTTTCCTGCGGGTCTTTCAGATGATCAATTTTAATTCCCTCCTGAAACTGAAGCAGGAT
CTGAAGAAGCAGCTGGGGGAAAACAGGATGGTGAGAAAGCACTTTCAGAACTC

Alignment

ORF - retro_cpor_1237 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.09 %
• Parental protein coverage: 89.36 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  HSINATQLMARIESYEGRDKKGISDVRRTFCLFVTFDLLFVTLLWIIELNVNGGIENTLEKEVVQYDYYS
          H...A.....R.....G.........RRTFCL.VTFDL.FV.LL..IEL.V....ENTLEK.VV..DY..
Retrocopy HQPHAAHSQDRVLQEKGEERR----IRRTFCLLVTFDL*FVILLQVIELHVKRSTENTLEKQVVW*DY-C

Parental  SYFDIFLLAVFRFKVLILAYAVCRLRHWWAIALTTAVTSAFLLAKVILSKLFSQGAFGYVLPIISFILAW
          SYF.IFLLAV.RFKV.ILA..V.RLRH.WA.AL.TAVT.AFLL.KV.LSKL.SQG.FG.VLPIISFILA.
Retrocopy SYFNIFLLAVSRFKVRILAHSVRRLRHSWAKALMTAVTRAFLLGKVVLSKLSSQGMFG*VLPIISFILA*

Parental  IETWFLDFKVLPQEAEE-ENRLLIVQDASERAALIPAGLSDGQFYSPPESEAGSDEQAEEKQDSEKALLE
          .ETWFLDFKVLP.EAEE.E...L.......R....PAGLSD.QF..PPE.EAGS.E.A..KQD.EKAL.E
Retrocopy LETWFLDFKVLPKEAEE>ETDSLVLR-MRRRGLPFPAGLSDDQF*FPPETEAGSEEAAGGKQDGEKALSE

Parental  L
          L
Retrocopy L

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	0.35 RPM	32.61 RPM
SRP017611_kidney	0.00 RPM	48.78 RPM
SRP017611_liver	0.00 RPM	7.40 RPM
SRP040447_lung	0.05 RPM	54.83 RPM
SRP040447_skeletal_muscle	0.20 RPM	7.97 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1237 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1237 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 10 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000038795	1 retrocopy	retro_btau_264,
Choloepus hoffmanni	ENSCHOG00000008990	1 retrocopy	retro_chof_984,
Callithrix jacchus	ENSCJAG00000012622	1 retrocopy	retro_cjac_3042,
Cavia porcellus	ENSCPOG00000004394	1 retrocopy	retro_cpor_1237 ,
Dasypus novemcinctus	ENSDNOG00000017960	1 retrocopy	retro_dnov_2389,
Equus caballus	ENSECAG00000005250	1 retrocopy	retro_ecab_709,
Microcebus murinus	ENSMICG00000000945	1 retrocopy	retro_mmur_388,
Macaca mulatta	ENSMMUG00000023659	1 retrocopy	retro_mmul_2643,
Ictidomys tridecemlineatus	ENSSTOG00000014750	1 retrocopy	retro_itri_286,
Tursiops truncatus	ENSTTRG00000004099	1 retrocopy	retro_ttru_864,