RetrogeneDB ID: retro_rnor_2176

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 5:144277101..144277905(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000012595
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Twf1
• Ensembl ID: ENSRNOG00000022507
• Aliases: Twf1, Ptk9
• Description: Twinfilin-1 [Source:UniProtKB/Swiss-Prot;Acc:Q5RJR2]

Sequence

>retro_rnor_2176
TGGATATGCATTGCATGGTCTCCAGATCATTCTCATGTTCGTCAAAAAATGCTGTATGCGGCAACAAGAGCAACTCTGAA
AAAAGAATTTGGAGGTGGCCACATTAAAGATGAAGTGTTTGGAACAGTAAAGGAGGACGTATCACTACATGGATATAGAA
AGTATCTTCTCTCCCAGTCTTCTCCTGCCCCTCTGACTGCAGCAGAGGAAGAATTAAGGCAGATTAAAATCAGTGAGGTA
CAAACTGACGTGAGTGTGGACACAAAGCATCAGACACTACAAGGAGTAGCATTTCCTATTTCTCGAGATGCCTTCCAGGC
TTTGGAAAAACTGAGTAAGAGACAGCTCAACTATGTGCAGTTGGAAATAGATATAAAAAATGAAACAATAATTTTGGCCA
ACACAGAAAATACAGAACTAAAAGATTTGCCAAAGAGGATTCCCAAGGATTCAGCACGCTACCATTTCTTTCTGTATAAG
CATTCCCACGAAGGAGACTACTTAGAGTCTGTAGTTTTTATTTATTCAATGCCCGGATACACGTGCAACATAAGAGAGCG
GATGCTGTATTCCAGCTGCAAGAGCCCTCTGTTAGATATTGTAGAAAGACAACTGCAGATGGATGTGATCAGAAAGATTG
AGATAGACAATGGGGATGAACTGATGGCAGATTTCCTGTACGATGAAGTCCATCCCAAGCAGCATGCACATAAGCAGAGT
TTTGCTAAACCAAAGGGTCCTGCGGGAAAGAGAGGGATTAGAAGATTGATTAGGGGTCCAGCGGAAGCAGAAGCCACTAC
TGAT

Alignment

ORF - retro_rnor_2176 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.51 %
• Parental protein coverage: 76.57 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  WIFIAWSPDHSHVRQKMLYAATRATLKKEFGGGHIKDEVFGTVKEDVSLHGYRKYLLSQSSPAPLTAAEE
          WI.IAWSPDHSHVRQKMLYAATRATLKKEFGGGHIKDEVFGTVKEDVSLHGYRKYLLSQSSPAPLTAAEE
Retrocopy WICIAWSPDHSHVRQKMLYAATRATLKKEFGGGHIKDEVFGTVKEDVSLHGYRKYLLSQSSPAPLTAAEE

Parental  ELRQIKISEVQTDVSVDTKHQTLQGVAFPISRDAFQALEKLSKRQLNYVQLEIDIKNETIILANTENTEL
          ELRQIKISEVQTDVSVDTKHQTLQGVAFPISRDAFQALEKLSKRQLNYVQLEIDIKNETIILANTENTEL
Retrocopy ELRQIKISEVQTDVSVDTKHQTLQGVAFPISRDAFQALEKLSKRQLNYVQLEIDIKNETIILANTENTEL

Parental  KDLPKRIPKDSARYHFFLYKHSHEGDYLESIVFIYSMPGYTCSIRERMLYSSCKSPLLDIVERQLQMDVI
          KDLPKRIPKDSARYHFFLYKHSHEGDYLES.VFIYSMPGYTC.IRERMLYSSCKSPLLDIVERQLQMDVI
Retrocopy KDLPKRIPKDSARYHFFLYKHSHEGDYLESVVFIYSMPGYTCNIRERMLYSSCKSPLLDIVERQLQMDVI

Parental  RKIEIDNGDELTADFLYDEVHPKQHAHKQSFAKPKGPAGKRGIRRLIRGPAEAEATTD
          RKIEIDNGDEL.ADFLYDEVHPKQHAHKQSFAKPKGPAGKRGIRRLIRGPAEAEATTD
Retrocopy RKIEIDNGDELMADFLYDEVHPKQHAHKQSFAKPKGPAGKRGIRRLIRGPAEAEATTD

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	27.32 RPM
SRP017611_kidney	0.14 RPM	86.04 RPM
SRP017611_liver	0.07 RPM	20.44 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2176 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2176 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2176 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017332	1 retrocopy	retro_amel_1224,
Choloepus hoffmanni	ENSCHOG00000008386	5 retrocopies	retro_chof_1525, retro_chof_2013, retro_chof_2569, retro_chof_391, retro_chof_509,
Homo sapiens	ENSG00000151239	2 retrocopies	retro_hsap_1819, retro_hsap_4916,
Monodelphis domestica	ENSMODG00000018535	1 retrocopy	retro_mdom_167,
Mustela putorius furo	ENSMPUG00000000364	1 retrocopy	retro_mputfur_1629,
Mus musculus	ENSMUSG00000022451	1 retrocopy	retro_mmus_2961,
Nomascus leucogenys	ENSNLEG00000017931	1 retrocopy	retro_nleu_2877,
Otolemur garnettii	ENSOGAG00000007525	1 retrocopy	retro_ogar_1058,
Pan troglodytes	ENSPTRG00000004846	1 retrocopy	retro_ptro_3279,
Rattus norvegicus	ENSRNOG00000022507	1 retrocopy	retro_rnor_2176 ,
Rattus norvegicus	ENSRNOG00000048915	2 retrocopies	retro_rnor_1740, retro_rnor_1908,