RetrogeneDB ID: retro_rnor_535

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 1:237085396..237087028(+)
• Located in intron of: ENSRNOG00000046233

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_535
ATGATGCCCACACCTGTTATCCTGTTGAAAGAGGGTACTGATAGCTCCCAAGGCATCCCTCAGCTTGTGAGTAACATGAG
TGCCTGCGAAGTGATTGCTGAGGCTGTAAGAACCACTCTGGGTCCCCATGGCATGGACAAACTTATTGTGGATGGCCGAG
GCAAAGCAACAATTTCTAATGATGGGGCCACAATTCTGAAACTCCTTGATGTTGTCCATCCTGCAGCAAAGACATTAATG
GATATTGCCAAATCCCAAGACGCTGAGGTTGGTGATGGCACCACCTCAGTGACCCTGCTGGCTGCGGAGTTTCTGAAGCA
GGTGAAGCCCTACGTGGAGGAAGGTTTACACCCTCAGATCATCATCAGAGCCTTACTCACAGCCACCCAGTTGGCTGTTA
ATAAAATCAAAGAGATAGCTGTGACTGTGAAGAAGCAAGATAAAGTAGAACAGAGGAAGATGCTAGAGAAGTGTGCGATG
ACTGCTCTGAGCTCCAAGCTGATCTTCCAGCAGAAGGTCTTCTTTGCCAAGATGGTGGTTGATGCTGTGATGATGCTTGA
CAAGTTGCTGTAGCTTAAAATGATTGGCATCAAGAAGGTGCAGGGCGGAGCCCTGGAGGAGTCTCGACTGATGGCTGGTG
TTGCGTTCAAGAAGACGTTCTCTTATGCTGGGTTTGAAATGCAGCCCAAGAAGTATAAGAATCCCAAGATTGCCCTCTTA
AATGTTGAGCTTAAACTGAAAGCAGAGAAAGATAATGCTGAAATCAGGGTCCACACAGTGGAGGATTACCAGGCAATTGT
TGATTCCGAGTGGAACATTCTCTATGACAAGTTAGAGAAGATTCATCAGTCTGGAGCCAAAGTCATCTTGTCTAAACTCC
CTATTGGGGATGTGGCCACCCAGTACTTTGCTGATAGGGACATGTTCTGTGCTGGCCGTGTGCCTGAGGAGGATCTGAAG
AGGACGATGATGGCTTGTGGAGGCTCAATCCAAACCAGTGTGAATGCTCTGATTCCAGATGTGCTGGGCCGTTGCCAGGT
GTTTGAAGAGACCCAAATTGGAGGAGAGAGGTACAATTTCTTCACTGGCTGCCCTAAGGCCAAGACATGTACGATCATTC
TCCATGGTGGTGCTGAGCAGTTTATGGAGGAGACAGAGAGGTCCCTACATGATGCCATCATGATTGTGAGGAAGGCCATC
AAGAACGACTCTGTGGTGGCTGGTGGTAGAGCCACTGAGATGGAGCTTTCCAAATACCTGTGGGATTACTCAAGGACCAT
TCCAGGGAAACAGCAGCTGTTGATTGGTGCATATGCCAAGGCCCTGGAGATTATTCCACGACAGCTGTGTGACAACGCTG
GCTTTGATGCCACAAACATCCTTAATAAACTGCGGGCTCGACATGCACAGGAGGGTATGTGGTATGGGGTGGACATCAAC
AAGGAGGACATTGCTGACAACTTCCAGGCATTTGTGTGGGAGCCAGCCATGATGTGCATCAACACTCTGACAGCAGCTTC
TGAGGCTGCGTGCCTGATTGTGTCTGTGGATGAGACTATCAAGAACCCCCGCTCCACTGTGGATGCTCCAGCTCCAGCAG
CTGGCCGGGGCAGAGGCCAGGGCCGCTTCCAT

Alignment

ORF - retro_rnor_535 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.96 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MMPTPVILLKEGTDSSQGIPQLVSNISACQVIAEAVRTTLGPRGMDKLIVDGRGKATISNDGATILKLLD
          MMPTPVILLKEGTDSSQGIPQLVSN.SAC.VIAEAVRTTLGP.GMDKLIVDGRGKATISNDGATILKLLD
Retrocopy MMPTPVILLKEGTDSSQGIPQLVSNMSACEVIAEAVRTTLGPHGMDKLIVDGRGKATISNDGATILKLLD

Parental  VVHPAAKTLVDIAKSQDAEVGDGTTSVTLLAAEFLKQVKPYVEEGLHPQIIIRAFRTATQLAVNKIKEIA
          VVHPAAKTL.DIAKSQDAEVGDGTTSVTLLAAEFLKQVKPYVEEGLHPQIIIRA..TATQLAVNKIKEIA
Retrocopy VVHPAAKTLMDIAKSQDAEVGDGTTSVTLLAAEFLKQVKPYVEEGLHPQIIIRALLTATQLAVNKIKEIA

Parental  VTVKKQDKVEQRKMLEKCAMTALSSKLISQQKVFFAKMVVDAVMMLDELLQLKMIGIKKVQGGALEESRL
          VTVKKQDKVEQRKMLEKCAMTALSSKLI.QQKVFFAKMVVDAVMMLD.LL.LKMIGIKKVQGGALEESRL
Retrocopy VTVKKQDKVEQRKMLEKCAMTALSSKLIFQQKVFFAKMVVDAVMMLDKLL*LKMIGIKKVQGGALEESRL

Parental  VAGVAFKKTFSYAGFEMQPKKYKNPKIALLNVELELKAEKDNAEIRVHTVEDYQAIVDAEWNILYDKLEK
          .AGVAFKKTFSYAGFEMQPKKYKNPKIALLNVEL.LKAEKDNAEIRVHTVEDYQAIVD.EWNILYDKLEK
Retrocopy MAGVAFKKTFSYAGFEMQPKKYKNPKIALLNVELKLKAEKDNAEIRVHTVEDYQAIVDSEWNILYDKLEK

Parental  IHQSGAKVILSKLPIGDVATQYFADRDMFCAGRVPEEDLKRTMMACGGSIQTSVNALIPDVLGRCQVFEE
          IHQSGAKVILSKLPIGDVATQYFADRDMFCAGRVPEEDLKRTMMACGGSIQTSVNALIPDVLGRCQVFEE
Retrocopy IHQSGAKVILSKLPIGDVATQYFADRDMFCAGRVPEEDLKRTMMACGGSIQTSVNALIPDVLGRCQVFEE

Parental  TQIGGERYNFFTGCPKAKTCTIILRGGAEQFMEETERSLHDAIMIVRRAIKNDSVVAGGGAIEMELSKYL
          TQIGGERYNFFTGCPKAKTCTIIL.GGAEQFMEETERSLHDAIMIVR.AIKNDSVVAGG.A.EMELSKYL
Retrocopy TQIGGERYNFFTGCPKAKTCTIILHGGAEQFMEETERSLHDAIMIVRKAIKNDSVVAGGRATEMELSKYL

Parental  RDYSRTIPGKQQLLIGAYAKALEIIPRQLCDNAGFDATNILNKLRARHAQGGMWYGVDINNEDIADNFQA
          .DYSRTIPGKQQLLIGAYAKALEIIPRQLCDNAGFDATNILNKLRARHAQ.GMWYGVDIN.EDIADNFQA
Retrocopy WDYSRTIPGKQQLLIGAYAKALEIIPRQLCDNAGFDATNILNKLRARHAQEGMWYGVDINKEDIADNFQA

Parental  FVWEPAMVRINALTAASEAACLIVSVDETIKNPRSTVDAPAPAAGRGRGQGRFH
          FVWEPAM..IN.LTAASEAACLIVSVDETIKNPRSTVDAPAPAAGRGRGQGRFH
Retrocopy FVWEPAMMCINTLTAASEAACLIVSVDETIKNPRSTVDAPAPAAGRGRGQGRFH

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	0.07 RPM	134.16 RPM
SRP017611_kidney	0.07 RPM	116.47 RPM
SRP017611_liver	0.13 RPM	57.89 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_535 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_535 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_535 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,