RetrogeneDB ID: retro_cpor_441

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_155:2145787..2146235(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMBIM4
• Ensembl ID: ENSCPOG00000007728
• Aliases: None
• Description: transmembrane BAX inhibitor motif containing 4 [Source:HGNC Symbol;Acc:24257]

Sequence

>retro_cpor_441
ATGGCAGATCCTGACCTCCGCTATCCTCGTTCCTCGATAGAAGATGACTTCAACTATGGCAGCTGCGTGGCCTCTGCCAG
ACCACACATCTGAATGGCCCTTCTCTGAAAGTCTACAGTATCTTGCTCTCTACTCCAGTAGCCTCTACAGTGTTTTTATA
CTTTGATTCTACATAAACATTTGTGCATGAAAGTCATGCCTTCGGAGTTTTGGGTTTGATCTTTGCACTGACTTTAAGCA
GACCTAAGCATCCCCTTAACCTGTACCTGACTCTTGGCTTTACCCTTCTGGAAACTCTGACTGTGGCAGTTGTAGTTATC
TTCTACAGTTATGTATTATTCTGAAAGCTTTTATATTGATTACTGCTGTGTTTCCTGGTTTGACTGTATATACTTTACAA
TTCAAGAGAGACTTCAGTAAATTTGGAGCAGGGCTGTTTGCTGTCCTG

Alignment

ORF - retro_cpor_441 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.73 %
• Parental protein coverage: 67.23 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MADPDSRYPRSSIEDDFNYGSCVASASLHIRMAFL-RKVYSILFLQVLLTTVTSTVFLYFESLRTFVHES
          MADPD.RYPRSSIEDDFNYGSCVASA..HI.MA.L..KVYSIL....L.T.V.STVFLYF.S..TFVHES
Retrocopy MADPDLRYPRSSIEDDFNYGSCVASARPHI*MALL<LKVYSIL----LSTPVASTVFLYFDST*TFVHES

Parental  PALILVFAIGALGLIFALTVNRHKHPLNLYLLFGFTLLEAVTVAVVVTFY-DVYIILQAFVLTTAVFLGL
          .A....F....L.....L....H...L.L.L.F.......V.V.V...FY....IIL.AF.L.TAVF.GL
Retrocopy HA----FGVLGLIFALTLSRPKHPLNLYLTLGFTLLETLTVAVVVI--FY<QLCIILKAFILITAVFPGL

Parental  TVYTLQSKRDFSKFGAGLFAVL
          TVYTLQ.KRDFSKFGAGLFAVL
Retrocopy TVYTLQFKRDFSKFGAGLFAVL

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	0.17 RPM	12.88 RPM
SRP017611_kidney	0.00 RPM	52.03 RPM
SRP017611_liver	0.04 RPM	33.60 RPM
SRP040447_lung	0.08 RPM	21.19 RPM
SRP040447_skeletal_muscle	0.04 RPM	6.48 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_441 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_441 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 3 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014558	1 retrocopy	retro_cjac_521,
Cavia porcellus	ENSCPOG00000007728	1 retrocopy	retro_cpor_441 ,
Tarsius syrichta	ENSTSYG00000010967	3 retrocopies	retro_tsyr_1322, retro_tsyr_1408, retro_tsyr_936,