RetrogeneDB ID: retro_cpor_497

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_17:5176925..5177930(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TUBB4B
• Ensembl ID: ENSCPOG00000011966
• Aliases: None
• Description: None

Sequence

>retro_cpor_497
ATGAGGGAAATTGCCCACTTGCAGGCTGGGCAGTACGGCAACCAGATTGGGGCCAAGTTCCGGGAGGTGATCAGGGATGA
GCATGACACTGACCCTGCTGGCACGTACCGTGGAGACAGCAACCTGCACTTGGAGCACATTAACATGTACTGCAAAAAGG
CCACAGGTGGCAAATACGTACCCCATGCTGCACTGGTGAACCTGGAGCCCGGGACCATGGACTCTGTACTCAGAGCTTTT
CAGGCGGATATTCAGGCCTGACAACTTTGTCTTCTGTCAAATTGCTTCTGGGAACAATGGGGGCAAAGAGCACTACACAG
AAGATGCAGAGCTGGTAGACTCAGTGCTAGATGTTGTGAGAAAGAAAAAGAGAGCTGGACTGCCTGCAGGGATTCTAGTT
AACCCACTCCTTAGGTGAGGGAACTGGGTGTGGGATGAGGAGGGTACCCTCCTCATCAGCAAGATCGGGAAGAGTTCCCA
GACTGGATCATGAACACATTCAGTATGATACCCTCACCCAATTAGACACACTGGTTGAGCCTTACAATGCCATCCTCTTA
GTCTACCAGCTTACAGAAAACACAGATGGAACCAACTGCATTGGTAACAAGGCCCTGTGTGACATCTGCTTCAGAGCCCT
AAAGCTCACCATGTCCAAATAAGGTGAATTGAATCACCTGGTGTCGGCCACCATGAGGGAGGTCACTGCCTGTCTGCGCT
TCCCTGGCCAGCTCAGTGCTGACCTGAGGAAGCTGGCTGTGGACATGGTGCCATTCCCCTGCCTGCACTCTTTCACGCCT
GGCTTTGCTGCTCTGACCAGCATGGCAGCCAACAGGTCAGGGCCTTGATGGTGCCTAAGCTCACCCAGCAGATGTTTGAT
GCCAAGAACACATGGCTGCCTGCGACCCCTGCCATGGCCACTACCTGACAGTGGCCACAATATAAAGGGGCCTCTTGTCC
ATGTAAGAGGTGGACAAACAGAAACATAATGTCCAAAACAACAAC

Alignment

ORF - retro_cpor_497 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.67 %
• Parental protein coverage: 75.73 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MREIVHLQAGQCGNQIGAKFWEVISDEHGIDPTGTYHGDSDLQLERINVYYNEATGGKYVPRAVLVDLE-
          MREI.HLQAGQ.GNQIGAKF.EVI.DEH..DP.GTY.GDS.L.LE.IN.Y...ATGGKYVP.A.LV.LE.
Retrocopy MREIAHLQAGQYGNQIGAKFREVIRDEHDTDPAGTYRGDSNLHLEHINMYCKKATGGKYVPHAALVNLE>

Parental  PGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVVRK-EAES-CDCLQGFQLTH
          PG......S..F..IFRPDNFVF.Q...GNN..K.HYTE.AELVDSVLDVVRK.E.ES..DCLQGF.LTH
Retrocopy PGPW-TLYSELFRRIFRPDNFVFCQIASGNNGGKEHYTEDAELVDSVLDVVRK<EKES<LDCLQGF*LTH

Parental  SLGGGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVVEPYNATLSVHQLVENTDETYCIDNEAL
          SLG.GTG.GM.....S..R.....R..............DT.VEPYNA.L.V.QL.ENTD.T.CI.N.AL
Retrocopy SLGEGTGCGMRRVPSSSARSGRVPRLDHEHIQYDTLTQLDTLVEPYNAILLVYQLTENTDGTNCIGNKAL

Parental  YDICFRTLKLTTPTYGDLNHLVSATMSGVTTCLRFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTS-R
          .DICFR.LKLT....G.LNHLVSATM..VT.CLRFPGQL.ADLRKLAV.MVPFP.LH.F.PGFA.LTS..
Retrocopy CDICFRALKLTMSK*GELNHLVSATMREVTACLRFPGQLSADLRKLAVDMVPFPCLHSFTPGFAALTS<H

Parental  GSQQYRALTVPELTQQMFDAKNM-MAACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKN
          GSQQ.RAL.VP.LTQQMFDAKN..MAACDP.HG.YLTVA...RG..SM.EVD.Q..NVQN.N
Retrocopy GSQQVRALMVPKLTQQMFDAKNT<MAACDPCHGHYLTVATI*RGLLSM*EVDKQKHNVQNNN

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	195.38 RPM
SRP017611_kidney	0.00 RPM	133.90 RPM
SRP017611_liver	0.00 RPM	58.33 RPM
SRP040447_lung	0.00 RPM	188.50 RPM
SRP040447_skeletal_muscle	0.00 RPM	131.03 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_497 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_497 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 8 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000011966	1 retrocopy	retro_cpor_497 ,
Microcebus murinus	ENSMICG00000010939	1 retrocopy	retro_mmur_792,
Macaca mulatta	ENSMMUG00000012164	2 retrocopies	retro_mmul_1849, retro_mmul_2533,
Monodelphis domestica	ENSMODG00000017213	1 retrocopy	retro_mdom_117,
Mus musculus	ENSMUSG00000036752	2 retrocopies	retro_mmus_158, retro_mmus_422,
Otolemur garnettii	ENSOGAG00000005927	2 retrocopies	retro_ogar_3410, retro_ogar_3450,
Pan troglodytes	ENSPTRG00000023373	2 retrocopies	retro_ptro_2403, retro_ptro_3166,
Rattus norvegicus	ENSRNOG00000010170	2 retrocopies	retro_rnor_742, retro_rnor_867,