RetrogeneDB ID: retro_cpor_174

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_1:34219535..34220132(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SCAMP1
• Ensembl ID: ENSCPOG00000008868
• Aliases: None
• Description: None

Sequence

>retro_cpor_174
TTGCCTAATATACCTAATACACAGCCAGAAATAGTGACACCAAAACAGGAACATCCAGCTTATACAGAGAATGCAAAGGA
ATATGTTCTTGCTCAAACTGAACTTCTAAAGCAGCAGGAAGAACTAGAAAGAAAAGCTGATAATTGAGGATAAGAAATGC
AAAACTTCAGTCAACATGGCAGAAAAAATAATTGGCCTCCTCTTTCCGAGAATTTTCCTGTGGGACTTTGTTTATATCAG
GACTTTTCTGTAGACATTCCTGTAGAATTTTGGAAGACAGTAAATCTCATACACTACTTGTGGATGCTCCATGCTGTAAC
ACTATTTCTGAATATCTTTAGATGTCTGGCTTGGTTTTTTGTTGATTCCTCAAGAGGGGTTGATTTTGAACTAAGTATCC
TGTGGTTTGTGCTGTTCACATCTTGCTCATTTGTCTGTTGGTATAGACCACTTTACAGAGCCTTCAAGAGTGACAATTCC
TTCAGATCCTTTGTGCTCTTCTTCATCTATATCTGTCACTTTGCTGTCCATGTGCTCCAGGCTTTAGGATTTTATAACTT
GGGCGATTGTGGTTGGGTTTCATCCCTTGTTGGTCTG

Alignment

ORF - retro_cpor_174 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.75 %
• Parental protein coverage: 59.76 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPNVPNTQPAIMKPTEEHPAYTQIAKEHALAQAELLKRQEELERKAAELDRREREMQNLSQHGRKNNWPP
          .PN.PNTQP.I..P..EHPAYT..AKE..LAQ.ELLK.Q...E......D....EMQN.SQHGRKNNWPP
Retrocopy LPNIPNTQPEIVTPKQEHPAYTENAKEYVLAQTELLKQQ---EELERKADN*G*EMQNFSQHGRKNNWPP

Parental  LPENFPVGPCFYQDFSVDIPVEFQKTVKLMYYLWMFHAVTLFLNIFGCLAWFFVDSSRGVDFGLSILWFV
          L.ENFPVG.C.YQDFSVDIPVEF.KTV.L..YLWM.HAVTLFLNIF.CLAWFFVDSSRGVDF.LSILWFV
Retrocopy LSENFPVGLCLYQDFSVDIPVEFWKTVNLIHYLWMLHAVTLFLNIFRCLAWFFVDSSRGVDFELSILWFV

Parental  LFTPCSFVCWYRPLYGAFRSDSSFRFFVFFFVYICQFAVHVLQAAGFHNWGNCGWISSLTGL
          LFT.CSFVCWYRPLY.AF.SD.SFR.FV.FF.YIC.FAVHVLQA.GF.N.G.CGW.SSL.GL
Retrocopy LFTSCSFVCWYRPLYRAFKSDNSFRSFVLFFIYICHFAVHVLQALGFYNLGDCGWVSSLVGL

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	0.06 RPM	48.03 RPM
SRP017611_kidney	0.00 RPM	10.05 RPM
SRP017611_liver	3.53 RPM	8.14 RPM
SRP040447_lung	0.00 RPM	9.89 RPM
SRP040447_skeletal_muscle	0.00 RPM	10.41 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_174 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_174 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 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000032395	1 retrocopy	retro_cfam_227,
Cavia porcellus	ENSCPOG00000008868	1 retrocopy	retro_cpor_174 ,
Homo sapiens	ENSG00000085365	1 retrocopy	retro_hsap_189,
Gorilla gorilla	ENSGGOG00000015191	1 retrocopy	retro_ggor_269,
Macaca mulatta	ENSMMUG00000016398	1 retrocopy	retro_mmul_396,
Monodelphis domestica	ENSMODG00000019731	1 retrocopy	retro_mdom_964,
Nomascus leucogenys	ENSNLEG00000012775	1 retrocopy	retro_nleu_1000,
Tarsius syrichta	ENSTSYG00000014113	1 retrocopy	retro_tsyr_1676,