RetrogeneDB ID: retro_rnor_755

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 10:57601941..57603024(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ankrd40
• Ensembl ID: ENSRNOG00000002935
• Aliases: None
• Description: ankyrin repeat domain-containing protein 40 [Source:RefSeq peptide;Acc:NP_001128171]

Sequence

>retro_rnor_755
ATGAGCGCCCTCCTACTGCAGAAGGAACAGCAGGAGAGGCTGCGGGAGGCAGCAGCCTTGGGGGACATTCGGGAGGTGGA
GAAACTGGTGGAGAGCGGGGTGGATGTGAACTCCCAAAATGAGGTCAATGGCTGGACCTGTTTACCCTGGGCATGTAAAC
GCAACCATGGGCAGGTGGTATCCTACCTGTTACAATCAGGGGCTGACAGAGAGATTCTTACAACAAAAGGAGAAATGCCG
GTACAATTAACATCAAAGAGAGAAATCAGGAAGATTATGGGAGTGGAAGAAGCTGATGATGATGACGAGATTCCCCAGCT
GAAGAAGGAGTGAGAACTGCCCTTTGTTCCCAACTACCTGGCCATCCCAGCCTTCCCTTTTATCTACACCCCTGCAGCAG
AAGACTCCACCCAGCTGCAGAATGGGAGCTCCTCCCCACCTCTGGTGTCTCCCCCTGAAGACGGCTCGTCTCCATTGCTT
TCCCCCACAGTGACCCCTCTGCTAGGAGCCTTTCCTAGGGACCACACCTCTTTGGCATTGGTCCAAAATGGTGATATTTC
TGCCCCCTCTGCCATACTTAGAACACCAGAAAGCACAAAACCTGGTCCTGTCTGTCAGCCACCAGTGAGTCAGAACCTGT
TCTCTGTCCCATCCAAGCCACCGGTGTCTCTGGAGCCTCAAAATGGGACATACGCAGGACCAGCGCCAGCATTCCAGCCA
TTTTTCTTCACCGGAGCATTTCCATTTAATATGCAAGAGGTGGTACTCAAGGTGAGGATTCAGAACCCATCTCTTCGTGA
AAATGACTTCATTGACATTGAACTGGATCGACAAGAACTCACCTACCAAGAACTGCTCAGAGTGAGTTGCTGTGAGCTGG
GTGTTAACCCAGACCAAGTGGAAAAGATAAGAAAGTTACCCAATACTCTGTTAAGAAAGGACAAAGATGTTGCACGACTC
CAGGACTTCCAGGAGCTGGAACTGGTTCTCACAATAAGTGAGAATAATTTTCTGTTTAGAAACCCTGCATCCTCACTGAC
TGAGAGCCCTTGCTTCAACCCGAGAGCTTCAAAACTGACATAC

Alignment

ORF - retro_rnor_755 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.66 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSALLEQKEQQERLREAAALGDIREVQKLVESGVDVNSQNEVNGWTCLHWACKRNHGQVVSYLLQSGADR
          MSALL.QKEQQERLREAAALGDIREV.KLVESGVDVNSQNEVNGWTCL.WACKRNHGQVVSYLLQSGADR
Retrocopy MSALLLQKEQQERLREAAALGDIREVEKLVESGVDVNSQNEVNGWTCLPWACKRNHGQVVSYLLQSGADR

Parental  EILTTKGEMPVQLTSRREIRKIMGVEEADDDEEIPQLKKESELPFVPNYLANPAFPFIYTPAAEDATQLQ
          EILTTKGEMPVQLTS.REIRKIMGVEEADDD.EIPQLKKE.ELPFVPNYLA.PAFPFIYTPAAED.TQLQ
Retrocopy EILTTKGEMPVQLTSKREIRKIMGVEEADDDDEIPQLKKE*ELPFVPNYLAIPAFPFIYTPAAEDSTQLQ

Parental  NGGPSPPPVSPPAEGSPPLLPPTEPPLLGAFPRDHTSLALVQNGDISAPSAILRTPESTKPGPVCQPPVS
          NG..SPP.VSPP..GS.PLL.PT..PLLGAFPRDHTSLALVQNGDISAPSAILRTPESTKPGPVCQPPVS
Retrocopy NGSSSPPLVSPPEDGSSPLLSPTVTPLLGAFPRDHTSLALVQNGDISAPSAILRTPESTKPGPVCQPPVS

Parental  QNRSLFSVPSKPPVSLEPQNGTYAGPAPAFQPFFFTGAFPFNMQELVLKVRIQNPSLRENDFIEIELDRQ
          QN..LFSVPSKPPVSLEPQNGTYAGPAPAFQPFFFTGAFPFNMQE.VLKVRIQNPSLRENDFI.IELDRQ
Retrocopy QN--LFSVPSKPPVSLEPQNGTYAGPAPAFQPFFFTGAFPFNMQEVVLKVRIQNPSLRENDFIDIELDRQ

Parental  ELTYQELLRVSCCELGVNPDQVEKIRKLPNTLLRKDKDVARLQDFQELELVLTISENNFLFRNPASSLTE
          ELTYQELLRVSCCELGVNPDQVEKIRKLPNTLLRKDKDVARLQDFQELELVLTISENNFLFRNPASSLTE
Retrocopy ELTYQELLRVSCCELGVNPDQVEKIRKLPNTLLRKDKDVARLQDFQELELVLTISENNFLFRNPASSLTE

Parental  RPCFNRRASKLTY
          .PCFN.RASKLTY
Retrocopy SPCFNPRASKLTY

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	93.68 RPM
SRP017611_kidney	0.07 RPM	56.80 RPM
SRP017611_liver	0.00 RPM	15.20 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_755 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_755 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_755 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000012574	1 retrocopy	retro_ecab_937,
Rattus norvegicus	ENSRNOG00000002935	2 retrocopies	retro_rnor_1835, retro_rnor_755 ,
Tursiops truncatus	ENSTTRG00000000221	1 retrocopy	retro_ttru_824,