RetrogeneDB ID: retro_rnor_2179

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 5:147727435..147728488(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Cct7
• Ensembl ID: ENSRNOG00000015630
• Aliases: None
• Description: T-complex protein 1 subunit eta [Source:RefSeq peptide;Acc:NP_001100073]

Sequence

>retro_rnor_2179
CTGAGGAAGCAGGATAAAGTAGAACAGAGGAAGATGCTTGAGAAGTGTGTGATGGCTGCCTGAGCTCCGAGCTGATCTCC
GGGCGGAAGGTCTTCGCCAAGATGGCGGCTTATGCGGTGATGATGCCTGACGAGGTGCTGCAGCTTACCGTGACTGGGCA
TCAAGAAGGTGCGGGGTGGAGCCCTGGAGGAGTCTCGGCAGGGGGCTGGTGCTGCGTTCGAGAAGACTTTCTCTTACGCT
GGGTTTGAAATGCAGCCCGAGAAGTCTAAGAACCCCAAGTCTGCCCTCCTCAACGTTGAGCTTGAGCGGAAAGCAGAGAA
AGATGATGCTGAAATCAGAGTCCACACGGGGGAGGATTTCCAGGCAATGATGGACACCAAGTGGAGCATTCGCTATGACA
AGTTAGAGAAGACCCATCAGTCTGGAGCCATCGTGTCTAAACTCCCTATTGGGGACGTGGCCATCCAGTACTCCGCTGAC
AGGGACGTGTTCTGTGCTGACTGCAAGCCTGAGGAGGATCTGAAGAAGACGATGACGGCTTGTGGAGGCTCAATCCAGTC
CAGTGTGGATGCTCTGACTCCAGATGTGCTGGGCTACTGCCAGGTGTTTGAAGAGACCCCAATTGGAGGAGAGAGACACA
ATTTCTTCACTGGCTGCCCCAAGGCCAAGACATGTACCAGCCTGCTCCATGGCGGTGCTGAGCAGTTCATGGAGGAGGCA
GAGAGGTCCCTACATGATGCCATCATAACTGTGAGGAGGGCCATCAAGAACGACTCTGTAGCGGCTGGTGGTGGAGTCAT
TGAGAGGGAGCTTTCCAAATACCTGCGGGATTAGTCAAGAACCATTTCTGGGAAACAGCAGCCATTGATCGGGGCATATG
CCAAGGCCCCAGAGGTTATTCCATGACAGCTATGTGACAATGCTGGTTTTGATGCCACAAACATCCTCAACAAACTGCAG
GCTGGACATGCACAGGGGGGCATGTGGTATGTGGTGGACATCAACAATAAGGACATCGCCCAAAACCTCCAGGCGTTTGT
GTGGGAGCCAGCT

Alignment

ORF - retro_rnor_2179 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.93 %
• Parental protein coverage: 65.07 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VKKQDKVEQRKMLEKCAMTA-LSSKLISQQKVFFAKMVVDAVMMLDELLQLKM-IGIKKVQGGALEESRL
          ..KQDKVEQRKMLEKC.M.A.LSS.LIS..KVF.AKM...AVMM.DE.LQL....GIKKV.GGALEESR.
Retrocopy LRKQDKVEQRKMLEKCVMAA<LSSELISGRKVF-AKMAAYAVMMPDEVLQLTV>LGIKKVRGGALEESRQ

Parental  VAGVAFKKTFSYAGFEMQPKKYKNPKIALLNVELELKAEKDNAEIRVHTVEDYQAIVDAEWNILYDKLEK
          .AG.AF.KTFSYAGFEMQP.K.KNPK.ALLNVELE.KAEKD.AEIRVHT.ED.QA..D..W.I.YDKLEK
Retrocopy GAGAAFEKTFSYAGFEMQPEKSKNPKSALLNVELERKAEKDDAEIRVHTGEDFQAMMDTKWSIRYDKLEK

Parental  IHQSGAKVILSKLPIGDVATQYFADRDMFCAGRVPEEDLKRTMMACGGSIQTSVNALIPDVLGRCQVFEE
          .HQSGA..I.SKLPIGDVA.QY.ADRD.FCA...PEEDLK.TM.ACGGSIQ.SV.AL.PDVLG.CQVFEE
Retrocopy THQSGA--IVSKLPIGDVAIQYSADRDVFCADCKPEEDLKKTMTACGGSIQSSVDALTPDVLGYCQVFEE

Parental  TQIGGERYNFFTGCPKAKTCTIILRGGAEQFMEETERSLHDAIMIVRRAIKNDSVVAGGGAIEMELSKYL
          T.IGGER.NFFTGCPKAKTCT..L.GGAEQFMEE.ERSLHDAI..VRRAIKNDSV.AGGG.IE.ELSKYL
Retrocopy TPIGGERHNFFTGCPKAKTCTSLLHGGAEQFMEEAERSLHDAIITVRRAIKNDSVAAGGGVIERELSKYL

Parental  RDYSRTIPGKQQLLIGAYAKALEIIPRQLCDNAGFDATNILNKLRARHAQGGMWYGVDINNEDIADNFQA
          RD.SRTI.GKQQ.LIGAYAKA.E.IP.QLCDNAGFDATNILNKL.A.HAQGGMWY.VDINN.DIA.N.QA
Retrocopy RD*SRTISGKQQPLIGAYAKAPEVIP*QLCDNAGFDATNILNKLQAGHAQGGMWYVVDINNKDIAQNLQA

Parental  FVWEPA
          FVWEPA
Retrocopy FVWEPA

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	134.16 RPM
SRP017611_kidney	0.00 RPM	116.47 RPM
SRP017611_liver	0.00 RPM	57.89 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2179 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2179 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2179 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000008879	1 retrocopy	retro_cfam_151,
Cavia porcellus	ENSCPOG00000019869	1 retrocopy	retro_cpor_1458,
Homo sapiens	ENSG00000135624	1 retrocopy	retro_hsap_3354,
Gorilla gorilla	ENSGGOG00000007766	1 retrocopy	retro_ggor_2274,
Macropus eugenii	ENSMEUG00000000416	1 retrocopy	retro_meug_1995,
Macaca mulatta	ENSMMUG00000012448	1 retrocopy	retro_mmul_2093,
Nomascus leucogenys	ENSNLEG00000010414	1 retrocopy	retro_nleu_1175,
Otolemur garnettii	ENSOGAG00000009162	2 retrocopies	retro_ogar_2001, retro_ogar_2698,
Pongo abelii	ENSPPYG00000012297	1 retrocopy	retro_pabe_2760,
Pan troglodytes	ENSPTRG00000012060	1 retrocopy	retro_ptro_2133,
Rattus norvegicus	ENSRNOG00000015630	2 retrocopies	retro_rnor_2179 , retro_rnor_535,
Tupaia belangeri	ENSTBEG00000002066	2 retrocopies	retro_tbel_3708, retro_tbel_3751,