RetrogeneDB ID: retro_cpor_285

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_118:3706514..3707274(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZSCAN4
• Ensembl ID: ENSCPOG00000005419
• Aliases: None
• Description: None

Sequence

>retro_cpor_285
ATGACTTTAGATCTCAGAAAATCATTTTGCCAAGAACCCTCCTCAGACAACCTTGAATCAGAAGATCTAGAATTTCCATC
TAGCCAAGATTTACCCAAAAAGAGAGATCTCTGCATTCTCAAGCATTCAACTCAACTCATTCAATGCAGTGATAACTCAG
GTGCAAGGAAGGAACTACAAAGATGCTATGAGTGTTTTCACTCCTGGTCGCAGGCAGAAAATCATAGCAAGGATGAGATT
ATTGCTCAGTTAGCCATGGAGTAGTTTATGCTGAGTGGCCGCTGCAAGGACAAGTCTATGTTGAAAAAAAATGGGAATCA
AGTGGTAAAAACCTGCAGAAGTTACTGGAAGACTTGACAGATGACTGTATGAAGCCACCGTGTTAGTCCATGTCTGCACG
CAGGGACAGGAAGCACCCTTCTCTGAGGATATGCCCTTGAAAGAAGTCATCATTCATCTCATGAAACAGTTGTCAGCAAA
AACCTTTACAGCAGAGAATCTGGGCACAGCCCACCAGGCTTCCCAAGATGCTCCTTTGGAAACAAGACAAGGACGTGAAC
ATGAAAAAGACTGCACTAGTGCCTGGGAAGTAACTCAAGTAAATGACCATATTACCAATCCAGGAAAAGAAACAGTTTCC
CTACTCACGATTCCAGAAGCAAATGATCCTATACCCTTAGAGGGAAGTGCTTCTTGGGAGAATACACACAGCTCCAGAAA
AGCAAGGCCAGACATGTGTGGATTGGAACCTTCTTACCAA

Alignment

ORF - retro_cpor_285 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.93 %
• Parental protein coverage: 76.19 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MALDLRKSFCQELSSNNLESEDLEFSSTQGFAVPK-REISAFSSIQLNS-LQYSDNSEARKELQRLYEFF
          M.LDLRKSFCQE.SS.NLESEDLEF.S.Q....PK.REISAFSSIQLNS..Q.SDNS.ARKELQR.YE.F
Retrocopy MTLDLRKSFCQEPSSDNLESEDLEFPSSQD--LPK>REISAFSSIQLNS<IQCSDNSGARKELQRCYECF

Parental  HSWLQPENHSKDQIIAQLAMEQFMLSGRCRDKSIL-KKKWESSGKNLEKLLEDLTDDCMKPP-VLVHVCM
          HSW.Q.ENHSKD.IIAQLAME.FMLSGRC.DKS.L....WESSGKNL.KLLEDLTDDCMKPP.VLVHVC.
Retrocopy HSWSQAENHSKDEIIAQLAME*FMLSGRCKDKSML<XXXWESSGKNLQKLLEDLTDDCMKPP<VLVHVCT

Parental  QGQEALFSEDMPLKEVIAHLTKQSSAKTFTA-GMGTAHQVSQNAPLGTRQGNEHEEDGCTSSWEVTQVND
          QGQEA.FSEDMPLKEVI.HL.KQ.SAKTFTA...GTAHQ.SQ.APL.TRQG.EHE.D.CTS.WEVTQVND
Retrocopy QGQEAPFSEDMPLKEVIIHLMKQLSAKTFTAENLGTAHQASQDAPLETRQGREHEKD-CTSAWEVTQVND

Parental  YITNPGKEIVSLLIIPEANDPTPVEESASWENTHSSRKARPVICGLQEESQ
          .ITNPGKE.VSLL.IPEANDP.P.E.SASWENTHSSRKARP..CGL....Q
Retrocopy HITNPGKETVSLLTIPEANDPIPLEGSASWENTHSSRKARPDMCGLEPSYQ

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	0.12 RPM
SRP017611_kidney	0.10 RPM	0.00 RPM
SRP017611_liver	0.00 RPM	0.00 RPM
SRP040447_lung	0.00 RPM	0.10 RPM
SRP040447_skeletal_muscle	0.00 RPM	0.00 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_285 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_285 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 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000005419	2 retrocopies	retro_cpor_1470, retro_cpor_285 ,
Dasypus novemcinctus	ENSDNOG00000011483	11 retrocopies	retro_dnov_1048, retro_dnov_1253, retro_dnov_1287, retro_dnov_1505, retro_dnov_174, retro_dnov_1780, retro_dnov_2499, retro_dnov_2556, retro_dnov_2666, retro_dnov_859, retro_dnov_964,
Equus caballus	ENSECAG00000015200	1 retrocopy	retro_ecab_78,
Loxodonta africana	ENSLAFG00000003257	1 retrocopy	retro_lafr_171,
Ictidomys tridecemlineatus	ENSSTOG00000023779	1 retrocopy	retro_itri_408,