RetrogeneDB ID: retro_cpor_1130

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_5:1561163..1562234(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TAF6
• Ensembl ID: ENSCPOG00000005116
• Aliases: None
• Description: None

Sequence

>retro_cpor_1130
TTCAGCACTTTCATCCCAGAGGGAGTCAGGGTCAATGTGGTTTAAAAGAACCTGCTCATGTATCTAATGTGCCTGGTCAA
GGCACTGATGGGCAACCCTACACTGTCTCTAGATAAATACGTGCATGAGCTGATTCCAGTGGTAATGACCTGCATTGTGA
GCAGACAGGTGTGTTTGTGACCTGATATTGACAATCAATGGGCACTCTGGGACTTTGCTGCCTGCCTAGTGGCCCAGATC
TATAAGCATTTCAGCACAACCACTAACAAGTCCCAGTCCCAAATCACAAAGACCTTCACAAAGAGCTTGCTAGACAAGAA
GACTACTTGGACAACTCATTATGGCTCCATTGCCAGCCTAGCAGAGCTGGGATATGATGTGATCAAGACTCTAATTATGC
CCAGGCTGTAGCAGGACAGGGAGCAGATCCACAGTGTCCTGGATGGCCCAGTGCTGAGTAACATGGACCATGTCAGAGCT
CACCATGTGCAGAGCCTCCTTCTGAAACACTGTGCACCTGTACTGGCTATGCTGCATGTCCTGCCTGATAATTAGGATGC
CTATCAGGCAGAATTTGGGTCCCTTGGGCCCCTCCGCTATTCCCATGTAATCAAGGCTCAGGTGCAGGCTGCTCAGCAGG
CACAGCAGGTCAACAGAACCAAACTGATCATCACACAGCCCTGACCCACACAGATCCTATCTCAGGCCCCTCAGTCTGGC
CCTCAGACTTCTGACTTGAAGGTCCTTGGCTCCACCATACTGCCCATCCAGACACTGACATCTGTGCTAGCTGCTGCCCC
ACCTCAGCCTTTCCCTCCTCTAACCAAGTTTTTTGTAAGATCGTCATCCTCTAGGGCCTCCTCCACACAGCAGATCTTGT
CCCTCAGCACCTCTGCCTCTGGCTCAGGATCTACCACTACCTCTCCTGTCACCACCGCAGTCCCCAGCATGTGGCCCATC
GTCAAGCTGGTCTCCACCAACTCCACTGCACCCTCCAGCAAGGTACCCTCTGCTCCTGGCAGTGTCCAGAAGTGCATGGT
AGTCTCACTACCCCCAACAGGAAATGGCAAG

Alignment

ORF - retro_cpor_1130 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.11 %
• Parental protein coverage: 53.1 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FSTFISEGVRVNVVQNNLALLIYLMRMVKALMDNPTLYLEKYVHELIPAVMTCIVSRQLCLRPDVDNHWA
          FSTFI.EGVRVNVV..NL..L.YLM..VKALM.NPTL.L.KYVHELIP.VMTCIVSRQ.CL.PD.DN.WA
Retrocopy FSTFIPEGVRVNVV*KNL--LMYLMCLVKALMGNPTLSLDKYVHELIPVVMTCIVSRQVCL*PDIDNQWA

Parental  LRDFAARLVAQICKHFSTTTNNIQSRITKTFTKSWVDEKTPWTTRYGSIAGLAELGHDVIKTLILPRLQQ
          L.DFAA.LVAQI.KHFSTTTN..QS.ITKTFTKS..D.KT.WTT.YGSIA.LAELG.DVIKTLI.PRL.Q
Retrocopy LWDFAACLVAQIYKHFSTTTNKSQSQITKTFTKSLLDKKTTWTTHYGSIASLAELGYDVIKTLIMPRL*Q

Parental  EGERIRSVLDGPVLSNIDRIGADHVQSLLLKHCAPVLAKLHPPPDNQDAYRAEFGSLGPLLCSHVVKARA
          ..E.I.SVLDGPVLSN.D...A.HVQSLLLKHCAPVLA.LH..PDN.DAY.AEFGSLGPL..SHV.KA..
Retrocopy DREQIHSVLDGPVLSNMDHVRAHHVQSLLLKHCAPVLAMLHVLPDN*DAYQAEFGSLGPLRYSHVIKAQV

Parental  QAALQAQQVNRTTLTITQPRPTLTLSQAPQSGPRTPGLLKVPGSIALPVQTLVSARAAAPPQPSPPPTKF
          QAA.QAQQVNRT.L.ITQP.PT..LSQAPQSGP.T...LKV.GS..LP.QTL.S..AAAPPQP.PP.TKF
Retrocopy QAAQQAQQVNRTKLIITQP*PTQILSQAPQSGPQTSD-LKVLGSTILPIQTLTSVLAAAPPQPFPPLTKF

Parental  IVMSSSSSASSTQQVLSLSTSAPGSGSTTTSPVTTTVPSVQPIVKLVSTASNAPPSTAPSGPGSVQKYIV
          .V.SSSS.ASSTQQ.LSLSTSA.GSGSTTTSPVTT.VPS..PIVKLVST.S.AP.S..PS.PGSVQK..V
Retrocopy FVRSSSSRASSTQQILSLSTSASGSGSTTTSPVTTAVPSMWPIVKLVSTNSTAPSSKVPSAPGSVQKCMV

Parental  VSLPPTGDGK
          VSLPPTG.GK
Retrocopy VSLPPTGNGK

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	53.49 RPM
SRP017611_kidney	0.00 RPM	47.21 RPM
SRP017611_liver	0.00 RPM	25.07 RPM
SRP040447_lung	0.00 RPM	64.21 RPM
SRP040447_skeletal_muscle	0.00 RPM	43.55 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1130 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1130 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	ENSCPOG00000005116	1 retrocopy	retro_cpor_1130 ,