RetrogeneDB ID: retro_cpor_1124

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_49:1017899..1018444(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM106C
• Ensembl ID: ENSCPOG00000008335
• Aliases: None
• Description: None

Sequence

>retro_cpor_1124
ATGGGGTTTCAGTATTCTTTCTCTGCTAGCCCTTCCTCCTCCAAGCAAAAGAAATATGGCAAGGCGGACATCCTGGCTGA
TCCTGAGCAAGAAAAAAGCCATTGCCCAGTTTCAATATGTCGAGTTCATAGGCAGAGATAGCATCACCTGTCTCACCTGC
CAAGGGACAGGCTACATTCCAACAGAGCAATTTATTGAAATTGATATCTTTGATCCCACACAGTGATCAGAGGTTTTACC
CTCAGAGAACTAAACAATATGTCTTTCTGTTGGTTCTGCTGTGCCTCCTGTCATTTAGTTTGGTGGTTTTCTTCCTGTTT
CCATATTCAGTCCTTGTAAATACTGATGGCATCAAAGTGGTTAAAGTCACATTTAATAAATAGGATTCCCTTGTAATCCT
TGTATCATGGCCACACTGAAAATCCGGAACTCCAACATCTACCCAGTGTCAGTAACCAGCCTGTCCAGCCAGGTTCCGTA
CATGAACACAGTAGTTGGCACAACATGTGACTATGAATGTCTCTCTCATTCTACCACAGTGAGAG

Alignment

ORF - retro_cpor_1124 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.76 %
• Parental protein coverage: 72.69 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MGSQHSASARLPSSKRKKDDREAFLADPEQEE-AIAQFPYVEFTGRDSITCLTCQGTGYIPTEQVNE-LV
          MG.Q.S.SA...SSK.KK......LADPEQE..AIAQF.YVEF.GRDSITCLTCQGTGYIPTEQ..E.L.
Retrocopy MGFQYSFSASPSSSKQKKYGKADILADPEQEK>AIAQFQYVEFIGRDSITCLTCQGTGYIPTEQFIE>LI

Parental  ALIPHSDQRLRPQRTKQYVLLSVLLCLLASGLVVFFLFPHSVLVNDDGIKVVKVTFNKRDSLVIL-AITA
          .LIPHSDQR..PQRTKQYV.L.VLLCLL...LVVFFLFP.SVLVN.DGIKVVKVTFNK.DSLVIL..I.A
Retrocopy SLIPHSDQRFYPQRTKQYVFLLVLLCLLSFSLVVFFLFPYSVLVNTDGIKVVKVTFNK*DSLVIL<CIMA

Parental  TLKIRNSNFYPVSVTSLSSQVQYMNTVVGT-YMTTNVSLILPRSE
          TLKIRNSN.YPVSVTSLSSQV.YMNTVVGT...T.NVSLILP..E
Retrocopy TLKIRNSNIYPVSVTSLSSQVPYMNTVVGT>HVTMNVSLILPQ*E

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	20.19 RPM
SRP017611_kidney	0.00 RPM	62.81 RPM
SRP017611_liver	0.00 RPM	26.73 RPM
SRP040447_lung	0.00 RPM	25.83 RPM
SRP040447_skeletal_muscle	0.00 RPM	5.09 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1124 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1124 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000008335	1 retrocopy	retro_cpor_1124 ,
Equus caballus	ENSECAG00000020351	1 retrocopy	retro_ecab_660,
Echinops telfairi	ENSETEG00000010370	1 retrocopy	retro_etel_173,
Myotis lucifugus	ENSMLUG00000017734	1 retrocopy	retro_mluc_1096,
Pteropus vampyrus	ENSPVAG00000014352	1 retrocopy	retro_pvam_562,
Sus scrofa	ENSSSCG00000028397	1 retrocopy	retro_sscr_473,
Tarsius syrichta	ENSTSYG00000001184	1 retrocopy	retro_tsyr_1263,