RetrogeneDB ID: retro_cpor_1320

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_7:31246044..31246541(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SUPT3H
• Ensembl ID: ENSCPOG00000024037
• Aliases: None
• Description: None

Sequence

>retro_cpor_1320
ATGAATAATACTGCAGCTAGCCCAATGTCTACCTCCATTTCGAGTAGTGGAAGAAGTACAGGGAAGTCGGTCAGCTTTGT
GGCAGAGTTGCAAAGTGTGATGTATTCGTTAGGTGATGCTTGGAGACCTCTTCATGAAACAGCAGTTTTGGTAGAAGATG
TGGTACACACTCAATTAATTAATCTGTTACAGCAAGCTGCTGAAATTCTCAGCTGAGGGGAGCAAGGGTAATCTCTGCAG
AAGATCTTCTGTTTTTGATGCGCAAAGATAAGAAAAAACTTAGAAGACTGCTGAAATATCTGTTCATGCGAGACTACAAA
TCAAAGATTATCAAAGGCATAGATGAGGATGAACTTCTGGAAGACAAAATGAGTGGTAGCAGTGTGAACAAAAGACAAAA
AATTGATCAAGACTTTCTCAGCTCTATTGACCAGACTGGAGAACTTTTAGCAATGTTTGAAGATGACAAGATTGATGAAG
TTAAACAAGAAAGAATG

Alignment

ORF - retro_cpor_1320 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.41 %
• Parental protein coverage: 51.55 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MNNTAASPMSTSISSSGRSTGKSVSFVAELQSMMYSLGDARRPLHETAVLVEDVVHTQLINLLQQAAEI-
          MNNTAASPMSTSISSSGRSTGKSVSFVAELQS.MYSLGDA.RPLHETAVLVEDVVHTQLINLLQQAAEI.
Retrocopy MNNTAASPMSTSISSSGRSTGKSVSFVAELQSVMYSLGDAWRPLHETAVLVEDVVHTQLINLLQQAAEI<

Parental  SQLRGARVISAEDLLFLMRKDKKKLRRLLKYMFMRDYKSKIIKGIDEDELLEDKLSGSSVNKRQKIDQDF
          SQLRGARVISAEDLLFLMRKDKKKLRRLLKY.FMRDYKSKIIKGIDEDELLEDK.SGSSVNKRQKIDQDF
Retrocopy SQLRGARVISAEDLLFLMRKDKKKLRRLLKYLFMRDYKSKIIKGIDEDELLEDKMSGSSVNKRQKIDQDF

Parental  LSSIDQTGELLAMFEDDEIDEVKQERM
          LSSIDQTGELLAMFEDD.IDEVKQERM
Retrocopy LSSIDQTGELLAMFEDDKIDEVKQERM

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	6.96 RPM
SRP017611_kidney	0.52 RPM	12.14 RPM
SRP017611_liver	0.13 RPM	6.62 RPM
SRP040447_lung	0.03 RPM	7.94 RPM
SRP040447_skeletal_muscle	0.00 RPM	2.78 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1320 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1320 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
Cavia porcellus	ENSCPOG00000024037	1 retrocopy	retro_cpor_1320 ,
Dasypus novemcinctus	ENSDNOG00000011043	1 retrocopy	retro_dnov_150,
Echinops telfairi	ENSETEG00000004704	1 retrocopy	retro_etel_1029,
Myotis lucifugus	ENSMLUG00000016339	1 retrocopy	retro_mluc_2262,
Oryctolagus cuniculus	ENSOCUG00000014574	1 retrocopy	retro_ocun_1724,