RetrogeneDB ID: retro_cpor_1106

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_46:11462612..11463250(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM105A
• Ensembl ID: ENSCPOG00000008574
• Aliases: None
• Description: None

Sequence

>retro_cpor_1106
AGAGATCATTATGATGCTCTAACATTAGTGCTGTTTCAGATATTCAACCAGGGCCTTTCTTTTCCATCCTGCATGAAGGA
GAAGGACATGCTTAAGCTTGCTGATAAACTGCTGTTTTCACAAGGTTGTAATTGGATCCAGCAATACAGTTTTGGTACTG
AGAAGTATACAAGTTCCAATGTGTTTGGAAAATTACATAAATGTGTACAACTGTGTAAGACCCATTGGACTAAATTTAGT
GAAATTAAGGATTATCACAAGAGAGGAAGCCTATGCAACATCACTTTTTCTGATGCCATTCTGGAATATAAGCTGTATGA
ACTTTAAAGTTCATCATGTTATATCAGGTCACTGAAGTTTATGAACAAATGAAGACTAAGAAGATCACTCCAAGTTTTTT
TAGATTCCTATTTTCCAGAGAAACCTCATCAGATACTTTGAACTTCATAATGAATCACCTGAATTTTATAGGTGACATAT
GTGGATTAGAGCAAATCCATATGTTTATACTGGAATACTCCCTTGAAGTGAAGATAAAAGTATTCCAACTGTTCAAGTTC
AACTCCAAAGACTTCACAGTGTGCTATCCGGAGAAGCCTCTCAGGGAGTGGCCCGAGGTCGCCCTGCTGACTGAAAAT

Alignment

ORF - retro_cpor_1106 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.37 %
• Parental protein coverage: 63.58 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RDHYDALRSVLFQIFSQGLSFPSWMKEKDIVKLPEKLLFSQGCNWIQQYSFGPEKYTGSNVFGKLRKCVE
          RDHYDAL..VLFQIF.QGLSFPS.MKEKD..KL..KLLFSQGCNWIQQYSFG.EKYT.SNVFGKL.KCV.
Retrocopy RDHYDALTLVLFQIFNQGLSFPSCMKEKDMLKLADKLLFSQGCNWIQQYSFGTEKYTSSNVFGKLHKCVQ

Parental  LLKTQWTEFSSIKDYHKRGSMCNILFSDAILEYKLYE-ALKFIMLYQVTEVYEQMKTNKIIPSLFRLLFS
          L.KT.WT.FS.IKDYHKRGS.CNI.FSDAILEYKLYE..LKFIMLYQVTEVYEQMKT.KI.PS.FR.LFS
Retrocopy LCKTHWTKFSEIKDYHKRGSLCNITFSDAILEYKLYE<TLKFIMLYQVTEVYEQMKTKKITPSFFRFLFS

Parental  RETSADPLSFMMNHLNSVGDTCGLEQIDMFILGYSLEVKIKVLRLFRFNSRDFAVCYPEEPLREWPEISL
          RETS.D.L.F.MNHLN..GD.CGLEQI.MFIL.YSLEVKIKV..LF.FNS.DF.VCYPE.PLREWPE..L
Retrocopy RETSSDTLNFIMNHLNFIGDICGLEQIHMFILEYSLEVKIKVFQLFKFNSKDFTVCYPEKPLREWPEVAL

Parental  LTED
          LTE.
Retrocopy LTEN

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	5.23 RPM
SRP017611_kidney	0.00 RPM	0.73 RPM
SRP017611_liver	0.00 RPM	0.74 RPM
SRP040447_lung	0.00 RPM	21.92 RPM
SRP040447_skeletal_muscle	0.00 RPM	0.50 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1106 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1106 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.

---

Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000008574	1 retrocopy	retro_cpor_1106 ,