RetrogeneDB ID: retro_cpor_691

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_234:795690..796564(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCPOG00000011784
• Aliases: None
• Description: None

Sequence

>retro_cpor_691
CATGAAGTTTCCAGGGCGACACCAACAAACAGCCAGCGCCCCAGGCCTCCAGAGGATTCTGACAGCGTTTCCAACTCCGA
TTCAGAAGACGAGAGCAGCATGAACTTTCTGGAAAAAAGGGCCTTAAATACAAAGCAAAACAAAGCCATGCTTGCAAATC
TCACGTCAGAATTAGAAAGTTTTCCTGGCTCATTCTCTGGAAGACCATCTGTCCCGGGCCCCCGATCACTGTCGAAGGCT
CCCCGGAGGCGCACGTTCCCACGCATGGCTGTCAGGGGGAACCCAGAGCGCAGAGCCGGCCGCCTGCCAGGTCCAGGTCT
CGGGTCCTGGGGTCTCTGAGTGCTGTCCCCACTGAGGAGGAGGAAGAAGAGGAAGATGATAAGTACATGCTCGTGAGGAA
AAGGAAGGCCTTGGATGCACTGGACGATGACATGCCCAGAAGTCGCCGCCCGGGATCCATGACCCTTCCACACATAATTC
GTCCGGTAGAAGAAATCACAGAGGACGAGTTGTAGACCATCTGCAGCACCTCCGGAGAGAAGATCTATAACCGCTCGCTG
GGCCCTACTTGCCATCAGTACCATCAGAAAACTATTGATACCAAAACAAACTGCAGGAACCCAGACTGCTGAGGCATTCG
AGGCCAGTTCTGTGGCCCTTGCCTTCGGAATCGCTATGGGGAGGAGTCAAGGATGCGCTGCTGGGCCCGGACTGGCACTG
CCCACCTTGTCGGGGGATCTGTAACTGCAGTTTCTGTCGCCAGCGAGATGGAGGGTGTGCAACTGGGGTCCTTGTGTATT
TAGCCAAATACCATGACTTTGGGCATGTGCATGCTTACTTGAAGAGTCTGAAACAGGAGTTTGAAATGCAAGTA

Alignment

ORF - retro_cpor_691 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.67 %
• Parental protein coverage: 79.89 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  HSTRATTNKKPAPPKPPENSDIISISDSEDESGVNFLEKRALNIKQNKAMLAKLMSELESFPGSFSGRPS
          H.....T......P.PPE.SD..S.SDSEDES..NFLEKRALN.KQNKAMLA.L.SELESFPGSFSGRPS
Retrocopy HEVSRATPTNSQRPRPPEDSDSVSNSDSEDESSMNFLEKRALNTKQNKAMLANLTSELESFPGSFSGRPS

Parental  VPGPRSLSKTPRRRTFPRMAARRNPERRA-RPLTRSRSRILGSLSALPTEEEEEEEDDKYMLVRKRKALD
          VPGPRSLSK.PRRRTFPRMA.R.NPERRA.RP..RSRSR.LGSLSA.PTEEEEEEEDDKYMLVRKRKALD
Retrocopy VPGPRSLSKAPRRRTFPRMAVRGNPERRA<RPPARSRSRVLGSLSAVPTEEEEEEEDDKYMLVRKRKALD

Parental  ALYSQDDDMPRSRRPGSMTLPHIIRPVEEITEDELENICSNSREKIYNRSLGSTCHQCRQKTIDTKTNCR
          AL...DDDMPRSRRPGSMTLPHIIRPVEEITEDEL..ICS.S.EKIYNRSLG.TCHQ..QKTIDTKTNCR
Retrocopy AL---DDDMPRSRRPGSMTLPHIIRPVEEITEDEL*TICSTSGEKIYNRSLGPTCHQYHQKTIDTKTNCR

Parental  NPDCWGIRGQFCGPCLRNRYGEE-VRDALLDPDWHCPPCRGICNCSFCRQRDGRCATGVLVYLAKYHGFG
          NPDC.GIRGQFCGPCLRNRYGEE.V.DALL.PDWHCPPCRGICNCSFCRQRDG.CATGVLVYLAKYH.FG
Retrocopy NPDC*GIRGQFCGPCLRNRYGEE<VKDALLGPDWHCPPCRGICNCSFCRQRDGGCATGVLVYLAKYHDFG

Parental  NVHAYLKSPHSLKQEFEMQV
          .VHAYLKS...LKQEFEMQV
Retrocopy HVHAYLKS---LKQEFEMQV

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	0.92 RPM
SRP017611_kidney	0.10 RPM	4.92 RPM
SRP017611_liver	0.04 RPM	12.14 RPM
SRP040447_lung	0.00 RPM	2.14 RPM
SRP040447_skeletal_muscle	0.01 RPM	0.64 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_691 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_691 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 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007809	1 retrocopy	retro_cjac_4087,
Cavia porcellus	ENSCPOG00000011784	2 retrocopies	retro_cpor_661, retro_cpor_691 ,
Homo sapiens	ENSG00000144354	1 retrocopy	retro_hsap_3438,
Mus musculus	ENSMUSG00000055612	2 retrocopies	retro_mmus_1493, retro_mmus_1494,
Nomascus leucogenys	ENSNLEG00000005787	1 retrocopy	retro_nleu_2295,
Pan troglodytes	ENSPTRG00000012645	1 retrocopy	retro_ptro_2331,
Ictidomys tridecemlineatus	ENSSTOG00000009026	1 retrocopy	retro_itri_369,