RetrogeneDB ID: retro_rnor_2164

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 5:103051075..103051897(+)
• Located in intron of: ENSRNOG00000037039

Retrocopy information

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

Parental gene information

• Parental gene symbol: Klf4
• Ensembl ID: ENSRNOG00000016299
• Aliases: Klf4, GKLF
• Description: Krueppel-like factor 4 [Source:RefSeq peptide;Acc:NP_446165]

Sequence

>retro_rnor_2164
GTTGGACCCAGAATACATTCCGCCACAGGTGGCGGGCTGATGGGCAAGCTTGTGCTGAAGGCGTCTCTGAGCACCCCTGG
CAGCGAGTACACCAGCCCTTCGGTCATCAGTGTTAGCAAAGGAAGCCCAGAGGGCAGCCTCCCTGTGGTAGTGGCGCCCT
ACAGCGGTGGCCCGCCGCGCATGTGCCCCAAGATTAAGCAAGAGGCCGTCCTGTCCTGCACGGTCAGCCCGTCCCTAGAG
GCCCACTTAAGCGCTGGACCCCAGCTCAGCAATGGCCACAGGCCCAATACACACGACTTCCCCCTGGGACGTCAGCTTCC
TACCAGGACTACCCCTACACTGAGTCCTGAGGAACTGCTGAACAGCAGGGACTGTCACCCTGGCCTGCCTCTTCCCCCAG
GATTCCATCCCCATCCGGGGCCCAGCTACCCTCCTTTCCTGCCAGACCAGATGCAGTCGTAAGTCTCCTCTCTCCATTAT
CAAGAGCTCATGCCACCGGGATCCTGCCTGCCAGAGGAGCCCAAGCCAAAGAGGGGAAGAAGGTCTTGGCCCAGGAAAAG
AATAGCCACCCACACTTGTGACTATGCAGGCTGTGGCAAAACCTATACGAAGAGTTCTCATCTCAAGGCACACCTGCGAA
CTCACACAGGCGAGAAACCTTACCACCGTGACTGGGACGGCTGTGGGTGGAAATTCGCCCGCTCAGATGAACTGACCAGG
CACTACCGCAAACACACCGGGCACCGGCCCTTTCAGTGCTAGAAGTGCAACAGGGCCTTTTCCAGGTCGGACCACCTTGC
TGTACACATGAAGAGGCACTTT

Alignment

ORF - retro_rnor_2164 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.7 %
• Parental protein coverage: 56.85 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IPPQQPQPPGGGLMGKFVLKASLSTPGSEYTSPSVISVSKGSPDGSHPVVVAPYSGGPPRMCPKIKQEAV
          ..P......GGGLMGK.VLKASLSTPGSEYTSPSVISVSKGSP.GS.PVVVAPYSGGPPRMCPKIKQEAV
Retrocopy VGPRIHSATGGGLMGKLVLKASLSTPGSEYTSPSVISVSKGSPEGSLPVVVAPYSGGPPRMCPKIKQEAV

Parental  PSCTVSRSLEAHLSAGPQLSNGHRPNTHDFPLGRQLPTRTTPTLSPEELLNSRDCHPGLPLPPGFHPHPG
          .SCTVS.SLEAHLSAGPQLSNGHRPNTHDFPLGRQLPTRTTPTLSPEELLNSRDCHPGLPLPPGFHPHPG
Retrocopy LSCTVSPSLEAHLSAGPQLSNGHRPNTHDFPLGRQLPTRTTPTLSPEELLNSRDCHPGLPLPPGFHPHPG

Parental  PSYPPFLPDQMQSQVPSLHYQELMPPGSCLPEEPKPKRGRRSWPRKRTATHTCDYAGCGKTYTKSSHLKA
          PSYPPFLPDQMQS.V.SLHYQELMPPGSCLPEEPKPKRGRRSWPRKR.ATHTCDYAGCGKTYTKSSHLKA
Retrocopy PSYPPFLPDQMQS*VSSLHYQELMPPGSCLPEEPKPKRGRRSWPRKRIATHTCDYAGCGKTYTKSSHLKA

Parental  HLRTHTGEKPYHCDWDGCGWKFARSDELTRHYRKHTGHRPFQCQKCDRAFSRSDHLALHMKRHF
          HLRTHTGEKPYH.DWDGCGWKFARSDELTRHYRKHTGHRPFQC.KC.RAFSRSDHLA.HMKRHF
Retrocopy HLRTHTGEKPYHRDWDGCGWKFARSDELTRHYRKHTGHRPFQC*KCNRAFSRSDHLAVHMKRHF

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	5.18 RPM
SRP017611_kidney	0.00 RPM	17.10 RPM
SRP017611_liver	0.00 RPM	1.82 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2164 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2164 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2164 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020355	1 retrocopy	retro_btau_521,
Pongo abelii	ENSPPYG00000019478	7 retrocopies	retro_pabe_1836, retro_pabe_2020, retro_pabe_2022, retro_pabe_2024, retro_pabe_2027, retro_pabe_2037, retro_pabe_3579,
Rattus norvegicus	ENSRNOG00000016299	1 retrocopy	retro_rnor_2164 ,
Ictidomys tridecemlineatus	ENSSTOG00000022002	1 retrocopy	retro_itri_1862,