RetrogeneDB ID: retro_cpor_755

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_26:23320290..23321157(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HAUS6
• Ensembl ID: ENSCPOG00000008053
• Aliases: None
• Description: None

Sequence

>retro_cpor_755
ATGAGCTCTGCCTGAGTCACTTCTGTTGAGAAGCAGCATTTCTGGACATATCTGTAGGTGCTCAGCTTCAAGCCAGGCCC
AGCTATCATGGTCCACAGGAAGATTTTGTTGCACACACAACTTGGAGTGAACATGTTGGATGAACTGAGCCATGATGCCT
TTCAAATAGTTTATTTTTGTTTCAAATGCTAGACCAGTCTCTCATCAAAGAAGTTTTCAAGTTTTGCTGATCTCCATTTG
ACTGAAAAGTGACACCAAATTCCAGAAACACTGTTGTGAATAGTTAAAAAATATGTCTGACAAATGTGAAAGTAGCTTTT
CTCAAGTCCTTGGCTCACTTTTTCTTTCTCTTGGTGGTTCTAAGTTTATTCATTTGATATATCATTTTGCAAGAGTTGTT
GCAATGAAATATATTGGGACCAATTTCAAAAGTTCTTCTCTACATTTTACAGAAACATTTAATATAAAGACACAAGATAT
GCACAAGTGCCTTTCCAGATATCATATAGCATGTAAGGAGTTTTATAAATTTTATAAAGAGAAGATTGTGTTGTCCAAAA
ATATCAGGAAAATGCCCAATTATCAGTTAAGCTAGTTCAGAATTTGAGACCAGTATATATAGGATTGCAAAACTAAATAA
AAAATGGAACCCTCTGATGAGTAAATATTATAAAAGAGAAAACTGAGAAGGTTCAATCTTTGTGGACCTAAGTAAATGAC
ATAAAGTTTTGGAAAGAGAAAGTGAAGTTCTTAATTTCAGTCCTTAGTCTTGTTAACCAATATGATTTAGATGGAAGTAA
TTTTGTTATTAATATTCTAAATCTCTTTCTTGACAAAACAGAGAAATAGATGTGACAGTTATTCATC

Alignment

ORF - retro_cpor_755 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.88 %
• Parental protein coverage: 53.28 %
• Number of stop codons detected: 12
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  MSSACVTSFEKQHLWMYLRALGFEPGRAAVASGKIVSHTHLGVNMFDKLNRDAFHIVSYF-LFQTLDQSL
          MSSA.VTS.EKQH.W.YL..L.F.PG.A.....KI..HT.LGVNM.D.L..DAF.IV.YF.LFQ.LDQSL
Retrocopy MSSA*VTSVEKQHFWTYL*VLSFKPGPAIMVHRKILLHTQLGVNMLDELSHDAFQIV-YF<LFQMLDQSL

Parental  TKEVFKFCWPPFD-QKSDTEFRKHCCEWLKKISAECD-SFPQVVGSLFLSPGGPKFIHLMYHFARYVAIK
          .KEVFKFC..PFD..KSDT.F.KHCCE.LK..S..C..SF.QV.GSLFLS.GG.KFIHL.YHFAR.VA.K
Retrocopy IKEVFKFC*SPFD<LKSDTKFQKHCCE*LKNMSDKCESSFSQVLGSLFLSLGGSKFIHLIYHFARVVAMK

Parental  YIKANSKNSSLHFSETCNVKTQDMHKCLARCLIARNRF-LQILQREDCVIRKYHENAQLSVKQLRNLRSE
          YI..N.K.SSLHF.ET.N.KTQDMHKCL.R..IA...F.L.IL.REDCV..KY.ENAQLSVK...NLR..
Retrocopy YIGTNFKSSSLHFTETFNIKTQDMHKCLSRYHIACKEF<L*IL*REDCVVQKYQENAQLSVKLVQNLRPV

Parental  YIGLQNQI-KKMEP-SDDQSILKEKI-EKVRSLWTLVNETLMVLEKEREVVNSVLSLVNQYDLDGSNVVI
          YIGLQN.I.KK..P.SD.....K.K..EKV.SLWT.VN......EK......SVLSLVNQYDLDGSN.VI
Retrocopy YIGLQN*I<KKWNP<SDE*IL*KRKL<EKVQSLWT*VNDIKFWKEKVKFLI-SVLSLVNQYDLDGSNFVI

Parental  NIPSLLLDKIEKQMGQLHI
          NI..L.LDK.EK.M.QL.I
Retrocopy NILNLFLDKTEK*M*QLFI

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	0.00 RPM	5.00 RPM
SRP017611_kidney	0.00 RPM	5.44 RPM
SRP017611_liver	0.00 RPM	3.44 RPM
SRP040447_lung	0.00 RPM	5.42 RPM
SRP040447_skeletal_muscle	0.00 RPM	1.94 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_755 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_755 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000008053	1 retrocopy	retro_cpor_755 ,