RetrogeneDB ID: retro_cpor_883

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_31:4362109..4362989(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLU7
• Ensembl ID: ENSCPOG00000004484
• Aliases: None
• Description: None

Sequence

>retro_cpor_883
ATTCCTCTGTATATTTCGTCAATGCCATAGTACACTAATCCATAAAAAAGACCACCTTAAAGCATCAGAGACCACAGGCA
GAAAAACAGAAGTAATTTAGTGCATCTGGTGAATGATACAAGAGAGTTGTAAAACAGAATTCCACAATGACTAAGTACTG
CAAAAGGACGTGTGAAAAGTGTAGGATCATGTCACACAAAAAGAAAGACTGCTTGGAGAGACGTAGGCAAGTTGGAGCCA
AATTTAGAGGTACTAACCTAGTTCCAGATGAACAAGTCCAGCCTCAGTTGCTGTTTAATACGATGGGAAGAGAGATTGGT
GAAATGGCTGTAATCCAGAAGAACCCATGAAAATTGTGGAAGAGTATGCCAAAATTGACCTGACAAAACAAACACTGAAA
GCCCAGAAACTCCAAGAAGAATTAGCTTCAGGAAAATTAGTAGAACAAGCTAATTCTCCAAAAATACCAGTGGCGGGAAG
AGGAACCAAATTCTCAGATGGAAAAAGATCCTAATAGCAAAGATGAAGATAAGTATGCAGATAACACTGACGTGTCTGGA
CAGAATTTTGACTCCAAGAGACGAATCACTGTTCGGAATCTCAGAATTTGAGAAGATATTGCAAAATATTTGAGAAATTT
GTATCCAAATTCTGCCTATTATGATCCAAAAACTAGAACAATGAGGGCTCCACATGCCAATTCAGGGAAGAGTCTAGATG
ATGTGAGTTACACTGGAGATAACTTCGTTAGGTACACAGGAAATACTATTTCAATGGCTCAGACACAGTTGTTTGCTTGA
GAAGCCTAAGACAGAGGATCTGAAGGCATCTTCAGGCAGACTCTATAAATCTAGAGCTGCTATATAAGTCCTTCAAAGTC

Alignment

ORF - retro_cpor_883 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.41 %
• Parental protein coverage: 50.68 %
• Number of stop codons detected: 8
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  IPQYISSVPWYIDPSKRP-TLKHQRPQPEKQKQFSSSGEWYKRGVKENSITTKYRKGACENCGAMTHKKK
          IP.YISS.P.Y..P.KRP.TLKHQRPQ.EKQK.FS.SGE.YKR.VK.NS..TKY.K..CE.C..M.HKKK
Retrocopy IPLYISSMP*YTNP*KRP<TLKHQRPQAEKQK*FSASGE*YKRVVKQNSTMTKYCKRTCEKCRIMSHKKK

Parental  DCFERPRRVGAKFTGINIAPDEHIQPQLMFD-YDGKRDRWNGYNPEEHMKIVEEYAKVDLAKRTLKAQKL
          DC.ER.R.VGAKF.G.N..PDE..QPQL.F..YDGKRD..NG.NPEE.MKIVEEYAK.DL.K.TLKAQKL
Retrocopy DCLERRRQVGAKFRGTNLVPDEQVQPQLLFN<YDGKRDW*NGCNPEEPMKIVEEYAKIDLTKQTLKAQKL

Parental  QEELASGKLVEQANSP-KHQWGEEEPNSQMEKDHNSEDEDEDKYADDIDMPGQNFDSKRRITVRNLRIRE
          QEELASGKLVEQANSP.K.QW.EEEPNSQMEKD.NS...DEDKYAD..D..GQNFDSKRRITVRNLRI.E
Retrocopy QEELASGKLVEQANSP>KYQWREEEPNSQMEKDPNS--KDEDKYADNTDVSGQNFDSKRRITVRNLRI*E

Parental  DIAKYLRNLDPNSAYYDPKTRAMRENPYANAGKNPDEVSYAGDNFVRYTGDTISMAQTQLFAWEAYDRGS
          DIAKYLRNL.PNSAYYDPKTR.MR..P.AN.GK..D.VSY.GDNFVRYTG.TISMAQTQLFA.EA.DRGS
Retrocopy DIAKYLRNLYPNSAYYDPKTRTMRA-PHANSGKSLDDVSYTGDNFVRYTGNTISMAQTQLFA*EA*DRGS

Parental  E-VHLQADPTKLELLYKSFKV
          E..HLQAD...LELLYKSFKV
Retrocopy E<RHLQADSINLELLYKSFKV

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	31.75 RPM
SRP017611_kidney	0.00 RPM	31.62 RPM
SRP017611_liver	0.04 RPM	22.16 RPM
SRP040447_lung	0.00 RPM	35.01 RPM
SRP040447_skeletal_muscle	0.00 RPM	12.89 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_883 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_883 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 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000004484	1 retrocopy	retro_cpor_883 ,
Dipodomys ordii	ENSDORG00000006239	3 retrocopies	retro_dord_125, retro_dord_140, retro_dord_563,
Ficedula albicollis	ENSFALG00000013473	1 retrocopy	retro_falb_12,
Myotis lucifugus	ENSMLUG00000003091	2 retrocopies	retro_mluc_2250, retro_mluc_2251,
Oryctolagus cuniculus	ENSOCUG00000011743	1 retrocopy	retro_ocun_818,
Otolemur garnettii	ENSOGAG00000012301	1 retrocopy	retro_ogar_1519,
Sorex araneus	ENSSARG00000012209	2 retrocopies	retro_sara_409, retro_sara_731,