RetrogeneDB ID: retro_rnor_2392

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 6:112102602..112104165(-)
• Located in intron of: ENSRNOG00000000345

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ppil2
• Ensembl ID: ENSRNOG00000026900
• Aliases: None
• Description: peptidyl-prolyl cis-trans isomerase-like 2 [Source:RefSeq peptide;Acc:NP_001017383]

Sequence

>retro_rnor_2392
ATGGGGAAGCGACAGCACCAGAAGGACAAGATGTACATCACCTGTGCCGAGTACATTCATTTCTATGGTGGCAGGAAGCC
AGATATCACACAGACAAGTTTTCGCCGCTTACCTTTTGACCACTGCAGTCTCTCTCTCCAGCCTTTTGTCTACCCAGTCT
GCACCCCGGAAGGTGTTGTCTTTGACTTGCTGAACATTGTCCCATGGCTTAAGAAGTATGGGACCAATCCGAGCACTGGA
GAGAAACTTGATGGGAAGTCCCTGATTAAGCTGAACTTTGCGAAGAACAGTGAAGGGCAGTACCACTGTCCAGTGCTGTA
CTCCGTGTTCACTGACAACATCCACATTGTGGCCATCAGGACAACTGGCAATGTCTACACCTATGAGGCAGTGGAGCAGC
TAAACATCAAGGCCAAGAACTTGAGGGACCTGTTAACTGATGAGCCCTTTTCCAGGCAAGACATCATCACCCTGCAGGAC
CCCACCAATTTGGACAAATTTAACGTTAGCAGCTTCTTCCATGTGAAGAATAACATGCGAACGATAGATCCAGATGAGGA
AAAGGCCAAACAAGACCCATCTTATTATTTGAAAAATACAAATGCGGAGACCCGAGAGACGCTACAGGAGCTCTACAAAG
AGTTCAAAGGAGATGAGATTTTAGCAGCTACCATGAAGCCACCTGAGAAGAAGAAGGTGGACCAACTAAATGCTGCCCAC
TACTCCACAGGGAAGGTCAGCGCGTCCTTCACCTCTACCGCCATGGTGCCTGAGACCACGCACGAAGCAGCTGTCATTGA
TGAAGATGTCCTGCGCTACCAGTTTGTGAAGAAGAAGGGCTATGTGAGGCTACATACCAACAAGGGCGACCTCAACCTAG
AGCTGCACTGTGACCTGACACCAAGAACCTGTGAAAACTTCATCAAGCTCTGCAAGAAACAGTATTATGATGGTACCATC
TTTCACAGGTCCATCAGGAACTTTGTGATCCAGGGTGGTGACCCTACAGGTACAGGCACGGGTGGAGAGTCATACTGGGG
CAAGCCTTTCAAAGATGAGTTCCGTCCCAATCTTTCACACACAGGCCGTGGGGTGCTCAGCATGGCCAATTCGGGGCCCA
ACACCAACAAGTCTCAGTTCTTCATCACCTTCCGGTCCTGTGCTTACCTGGATAAGAAGCATACCATCTTTGGACGGGTT
GTCGGGGGCTTTGACACGCTGACAGAGATGGAGAATGTGGAGAGTGACCCCAAAACTGACCGCCCTAAGGAAGAAGTGCA
CATCTGTACAACCACCGTGTTTGTGGATCCCTATGAGGAGGCCGATGCCCAGATTGCCCAGGAACGGAAGAAGACACAGC
ACCAAGTGGATCCAGAGGCCAAGGCCAAGAAGAAACAGCCCCAGCCTGGAAACCAGGGTCCCCCGACATACTGCCGGGGG
GTGGGCAAGTATATCAACCCTGCAGCCACAAAACGAGCAGCAGAGGAAGAACCATCCACCAGCACAGCCATCCCCACAGT
CAAGAAAAGGCCCAGTCGGGGCTTTGGGGACTTCAGCTCCTGG

Alignment

ORF - retro_rnor_2392 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.5 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGKRQHQKDKMYITCAEYTHFYGGRKPDITQTSFRRLPFDHCSLSLQPFVYPVCTPEGVVFDLLNIVPWL
          MGKRQHQKDKMYITCAEY.HFYGGRKPDITQTSFRRLPFDHCSLSLQPFVYPVCTPEGVVFDLLNIVPWL
Retrocopy MGKRQHQKDKMYITCAEYIHFYGGRKPDITQTSFRRLPFDHCSLSLQPFVYPVCTPEGVVFDLLNIVPWL

Parental  KKYGTDPSTGEKLDGKSLIKLNFAKNSEGQYHCPVLYSVFTDNTHIVAIRTTGNVYTYEAVEQLNIKAKN
          KKYGT.PSTGEKLDGKSLIKLNFAKNSEGQYHCPVLYSVFTDN.HIVAIRTTGNVYTYEAVEQLNIKAKN
Retrocopy KKYGTNPSTGEKLDGKSLIKLNFAKNSEGQYHCPVLYSVFTDNIHIVAIRTTGNVYTYEAVEQLNIKAKN

Parental  LRDLLTDEPFSRQDIITLQDPTNLDKFNVSSFFHVKNNMRMIDPDEEKAKQDPSYYLKNTNAETRETLQE
          LRDLLTDEPFSRQDIITLQDPTNLDKFNVSSFFHVKNNMR.IDPDEEKAKQDPSYYLKNTNAETRETLQE
Retrocopy LRDLLTDEPFSRQDIITLQDPTNLDKFNVSSFFHVKNNMRTIDPDEEKAKQDPSYYLKNTNAETRETLQE

Parental  LYKEFKGDEILAATMKPPEKKKVDQLNAAHYSTGKVSASFTSTAMVPETTHEAAVIDEDVLRYQFVKKKG
          LYKEFKGDEILAATMKPPEKKKVDQLNAAHYSTGKVSASFTSTAMVPETTHEAAVIDEDVLRYQFVKKKG
Retrocopy LYKEFKGDEILAATMKPPEKKKVDQLNAAHYSTGKVSASFTSTAMVPETTHEAAVIDEDVLRYQFVKKKG

Parental  YVRLHTNKGDLNLELHCDLTPKTCENFIKLCKKQYYDGTIFHRSIRNFVIQGGDPTGTGTGGESYWGKPF
          YVRLHTNKGDLNLELHCDLTP.TCENFIKLCKKQYYDGTIFHRSIRNFVIQGGDPTGTGTGGESYWGKPF
Retrocopy YVRLHTNKGDLNLELHCDLTPRTCENFIKLCKKQYYDGTIFHRSIRNFVIQGGDPTGTGTGGESYWGKPF

Parental  KDEFRPNLSHTGRGVLSMANSGPNTNKSQFFITFRSCAYLDKKHTIFGRVVGGFDTLTAMENVESDPKTD
          KDEFRPNLSHTGRGVLSMANSGPNTNKSQFFITFRSCAYLDKKHTIFGRVVGGFDTLT.MENVESDPKTD
Retrocopy KDEFRPNLSHTGRGVLSMANSGPNTNKSQFFITFRSCAYLDKKHTIFGRVVGGFDTLTEMENVESDPKTD

Parental  RPKEEVRICTTTVFVDPYEEADAQIAQERKKTQHQVDPEAKAKTNQPQPGNQGPQTYRQGVGKYINPAAT
          RPKEEV.ICTTTVFVDPYEEADAQIAQERKKTQHQVDPEAKAK..QPQPGNQGP.TY..GVGKYINPAAT
Retrocopy RPKEEVHICTTTVFVDPYEEADAQIAQERKKTQHQVDPEAKAKKKQPQPGNQGPPTYCRGVGKYINPAAT

Parental  KRAAEEEPSTSTAIPTAKKRPSRGFGDFSSW
          KRAAEEEPSTSTAIPT.KKRPSRGFGDFSSW
Retrocopy KRAAEEEPSTSTAIPTVKKRPSRGFGDFSSW

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	26.60 RPM
SRP017611_kidney	0.07 RPM	28.19 RPM
SRP017611_liver	0.00 RPM	19.36 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2392 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2392 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2392 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
Loxodonta africana	ENSLAFG00000016750	1 retrocopy	retro_lafr_469,
Rattus norvegicus	ENSRNOG00000008489	1 retrocopy	retro_rnor_2911,
Rattus norvegicus	ENSRNOG00000026900	2 retrocopies	retro_rnor_1216, retro_rnor_2392 ,