RetrogeneDB ID: retro_cpor_350

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_13:22930664..22932015(-)
• Located in intron of: ENSCPOG00000013335

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZNF131
• Ensembl ID: ENSCPOG00000011858
• Aliases: None
• Description: None

Sequence

>retro_cpor_350
AAACAAAACTCTGCTCCTTTACAGGAAAAAATGAGGCAAAAAAAGAGAAAGATTACAGAAACTTAAAATGTTATCACTGA
ATCATTGCCATCTGCAGCATCAGAACCTGTGGAAATTAAGGTGGAGATTGCTGAAGGTACAATTGAAGTGGAAGATGAAA
AGCATTGAAATATTAGAGAAAGTGACATCTGCCATGCAGTCCATAAAGTACATTCAGAGCATAAGTTCCTCTGATGATTC
TGCTCTGGCGCTGTTGGCAGATATTAACACCAAATATCGTCAAGGTTATAGAAAAGGGCTGATTAAAGATGAAGATGGCT
GTGCATCTGACCCCATAAGCAAATAGTAACACATGAAATCACACTTCACTGAAGAGTTACAAATATGAGATGTGCCATAA
AAGGTATCTTTGGGAGGGTGCATGGAAACAACACCTAAATTGTTACCATCTTGAAAGAGATGAGGTCAGTAAGAAGAAAA
GAACTGGGGAAAAGATTCACATATGTCAGTATTGTGAGAAACAGTTTGATCACTTTGGACATTTTAAAGAGCATCTTTGA
AAACATACAGGTGGACAACCTTTTGAATGTCCAAATTGTCATGAACAGTTTGCTAGAAATAATACTCTGAAATGTCACCT
CATTGCATTCCAAACCAGAGTGGGAGCAAAAAAGGAAGAAAGAAGCTTTACAAATGTCAGGTCTGTAACAGTGTCTTCAG
TAGTTGGGACCAATTCAGAGATCACTTGGTAATATACACTGGGAATAAACCCAACCATTGCACTCTGTGTGACTTGTGGT
TTATGAAAGGAAATGAATTTAGGAAGCATCTAAATGAATCTCACAATATTTCAGAGCATCTGGTAACTAAAGAAGTCCTT
TCAATAGGAACACAAGTGCAAACCGAACCCGTGACATCAGTGACTATTATAAAACAGGTTGGGAAAGTGCATATGTTACC
ACTGCTTCAGGTTCAAGTGGATTCAGCACAAATGACTATGGAACAAGTTCAATCAGATCTGCTCCAGGATGGCCAGGTAC
ATGATTCACATATGAGTGAGCTTCCAGAGCAGGTCAAGTGAGCTATCTAGAAGTGAGCTGAATTCAGACTGAAGAAGGAA
CTGAAGTACATGATGAGTTGCATGTTGAATGGATAAATCAATGCCAGTGGAAGTACAAATTGAACTTTTGGGAGCAGACT
TGGATCACGAGACCCCTGGAATCGTGAACCAAGAGGAGAGCGAGCCTAACCAAGCAGATGGTACTGAGCTTGCTGGGGAA
GATCTCGGAGGTGCTAAGGATTTAAAGACCAAACCAACAGTGGATCCCAAGCTGAAAAGACAGAGAATGAA

Alignment

ORF - retro_cpor_350 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.79 %
• Parental protein coverage: 76.62 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  KENSAPLEENTT---RKIAETSNVITESLPSAESEPVEIEVEIAEGTIEVEDE-GMETLEEVVSTKQSIK
          K.NSAPL.E......RKI.ET.NVITESLPSA.SEPVEI.VEIAEGTIEVEDE...E.LE.V.S..QSIK
Retrocopy KQNSAPLQEKMRQKKRKITET*NVITESLPSAASEPVEIKVEIAEGTIEVEDE>SIEILEKVTSAMQSIK

Parental  YIQSTGSSDDSALALLADITSKYRQGDRKGQIKDEDGCASDPINKQEHMKSHSTE-SFKCEICNKRYLRE
          YIQS..SSDDSALALLADI..KYRQG.RKG.IKDEDGCASDPI.K..HMKSH.TE.S.K.E.C.KRYL.E
Retrocopy YIQSISSSDDSALALLADINTKYRQGYRKGLIKDEDGCASDPISK**HMKSHFTE>SYKYEMCHKRYLWE

Parental  SAWKQHLNCYHLEEGGVSKKQRTGKKIHICQYCEKQFDHFGHFKEHLRKHTGEKPFECPNCHERFARNST
          .AWKQHLNCYHLE...VSKK.RTG.KIHICQYCEKQFDHFGHFKEHL.KHTG..PFECPNCHE.FARN.T
Retrocopy GAWKQHLNCYHLERDEVSKKKRTGEKIHICQYCEKQFDHFGHFKEHL*KHTGGQPFECPNCHEQFARNNT

Parental  LKCHLTACQTGVGAKK-GRKKLYECQVCNSVFNSWDQFKDHLVIHTGDKPNHCTLCDLWFMQGNEFRRHL
          LKCHL.A.QT.VGAKK.GRKKLY.CQVCNSVF.SWDQF.DHLVI.TG.KPNHCTLCDLWFM.GNEFR.HL
Retrocopy LKCHLIAFQTRVGAKK<GRKKLYKCQVCNSVFSSWDQFRDHLVIYTGNKPNHCTLCDLWFMKGNEFRKHL

Parental  NESHNISERLITEEVLSVETRVQTEPVTSMTIIEQVGKVHMLPLLQVQVDSAQVTVEQVHPDLLQDGQVH
          NESHNISE.L.T.EVLS..T.VQTEPVTS.TII.QVGKVHMLPLLQVQVDSAQ.T.EQV..DLLQDGQVH
Retrocopy NESHNISEHLVTKEVLSIGTQVQTEPVTSVTIIKQVGKVHMLPLLQVQVDSAQMTMEQVQSDLLQDGQVH

Parental  DSHMSELPEQV-QVSYLEVGRIQTEEGTEVHVEELHVERVNQ-MPVEVQTELLEADLDHVTPGIMNQEES
          DSHMSELPEQV.QVSYLEV..IQTEEGTEVH..ELHVE..NQ.MPVEVQ.ELL.ADLDH.TPGI.NQEES
Retrocopy DSHMSELPEQV<QVSYLEVS*IQTEEGTEVH-DELHVEWINQ<MPVEVQIELLGADLDHETPGIVNQEES

Parental  EPNQADGTETAGEDLEGAEGLKTKPTVD-SQAEKTESE
          EPNQADGTE.AGEDL.GA..LKTKPTVD.SQAEKTE.E
Retrocopy EPNQADGTELAGEDLGGAKDLKTKPTVD<SQAEKTENE

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	11.04 RPM
SRP017611_kidney	0.21 RPM	10.68 RPM
SRP017611_liver	0.00 RPM	7.36 RPM
SRP040447_lung	0.20 RPM	14.20 RPM
SRP040447_skeletal_muscle	0.04 RPM	6.77 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_350 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_350 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
Callithrix jacchus	ENSCJAG00000001280	1 retrocopy	retro_cjac_2484,
Cavia porcellus	ENSCPOG00000011858	1 retrocopy	retro_cpor_350 ,
Gorilla gorilla	ENSGGOG00000002252	1 retrocopy	retro_ggor_2485,
Ictidomys tridecemlineatus	ENSSTOG00000015383	1 retrocopy	retro_itri_1485,
Tursiops truncatus	ENSTTRG00000009644	1 retrocopy	retro_ttru_418,