RetrogeneDB ID: retro_cpor_676

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_22:4479255..4479811(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCPOG00000009142
• Aliases: None
• Description: None

Sequence

>retro_cpor_676
TCCTTGACCCATGGGGCTACTCCTGTACTCTGTTACCTGCGATCATCACTGCAGTGAATGCCTGTCTTTTTCTGGTGGCC
TTTGTGGCTGCTGTGGCACCTGAAAAAAGAACTACTATCTTATAATCTTTGCCATTTCCTGTCTCTTATGCTAGTGGAGG
TGGCCACAGCCATTGTTGGGTGTATTTTTAGAAACAAGGTGATATCAGAGTTTAATAAGGACTTCTGGCACCAGATACAG
ACTTACCCCTGAAACGGTGGCGCAGCCTCATTCTTGGAGAAACTGTAGGAAGAGTGGACATACTGGGGGCTGCTAACTAC
ACAGATTGGGAGAACAGCCCTAGCATGGCCAAGGGCTGAGTTCAGACTCCTCTGTTGGCATCACTGCAGGCTGTAGAACT
GATATCACTGTGTGTTCAATCTATACCCCGAGCTGTGTGGAGAAGATCGGGCTCTGGCTGAGGAAGGGTATGCTGTTGGT
AGCTGGAGCAGCCCTGGGCAATGCTTTTGTAGTTCAGGGAATTGTTTTTACTTGCTGCCTTGTAGAGTCGATGAAG

Alignment

ORF - retro_cpor_676 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.12 %
• Parental protein coverage: 76.71 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  TMSQGATPG-SLLPVIIIAVGAFLFLVAFI-GCCGACKENYCLMITFAI-FLTLIMLVELAIAIAGYVFR
          ....GATP...LLP.II.AV.A.LFLVAF..GCCG..K.NY.L.I.FAI.FL.L.MLVE.A.AI.G..FR
Retrocopy SLTHGATPV<TLLPAIITAVNACLFLVAFV<GCCGT*KKNYYLII-FAI<FLSL-MLVEVATAIVGCIFR

Parental  DKVRAEFNKDFRQQMQNYPKNNGTAAF-LDKLQTKFHCCGAANYTDWENIFGM-GKDRVPDSCCINVTMG
          .KV..EFNKDF..Q.Q.YP.N.G.A.F.L..........GAANYTDWEN...M.G.....DS.....T.G
Retrocopy NKVISEFNKDFWHQIQTYP*NGGAASF<LGETVGRVDILGAANYTDWENSPSM<GQGLSSDSS-VGITAG

Parental  CGTDFKLNFINTEGCVEKIGNWLRRNVLLVAAAALGIAFVEVLGIIFACCLVKSIR
          C.TD.....I.T..CVEKIG.WLR...LLVA.AALG.AFV.V.GI.F.CCLV.S..
Retrocopy CRTDITVCSIYTPSCVEKIGLWLRKGMLLVAGAALGNAFV-VQGIVFTCCLVESMK

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	37.50 RPM
SRP017611_kidney	0.00 RPM	167.92 RPM
SRP017611_liver	0.00 RPM	40.96 RPM
SRP040447_lung	0.00 RPM	301.64 RPM
SRP040447_skeletal_muscle	0.00 RPM	109.32 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_676 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_676 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000011931	1 retrocopy	retro_btau_234,
Callithrix jacchus	ENSCJAG00000007935	1 retrocopy	retro_cjac_4051,
Cavia porcellus	ENSCPOG00000000183	1 retrocopy	retro_cpor_716,
Cavia porcellus	ENSCPOG00000009142	1 retrocopy	retro_cpor_676 ,
Mus musculus	ENSMUSG00000025351	1 retrocopy	retro_mmus_1722,