RetrogeneDB ID: retro_rnor_2414

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 7:5720881..5722130(+)
• Located in intron of: ENSRNOG00000047228

Retrocopy information

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

Parental gene information

• Parental gene symbol: Psmc4
• Ensembl ID: ENSRNOG00000018994
• Aliases: Psmc4, Tbp7
• Description: 26S protease regulatory subunit 6B [Source:UniProtKB/Swiss-Prot;Acc:Q63570]

Sequence

>retro_rnor_2414
GAGATAGGCATTTTGGTGGAGAAAATTCAGGATGAGATGCCAGCACTGTCCGTGTCTCGGCTGCAGACTGGTCTGTCCTT
TCTGCAACCTGAACCTGAAGACCTGGAGGACGTATACAGCCTCTACAAGAAGCTGTAGCAAGAGCTGGAGTTCCTGGAGG
TGCAGGAGGAATATATCAAGGATGAACAGAAGAACCTGAAGAAGGAGTTCCTCCATGCCCAGGAGGAGGTAAAGCAAATC
CAGAGCATTCCGTTGGTCATTGGTCAGTTTTTGGAAGTTGTGGATCAGAACACAACCATTGTGGGCTCTACCACAGGCTC
TAACTGTTATGTGTGCATCCTGAGTACCATTGATCGGGAGCTGCTCAAACCCAATGCCTCAGTGACCCTCCACAAGCACA
GCAACGCACTGGTGAATGTGCTGCCTCCCGAGGCCGAAAGCAGCATCATGATGCTCACCTCAGACCAGAAGCCCAACGTG
ATGTACGCTGATACAGGAAGCATGGACATCCAGAAACAGGAGGTGCGGGAGGCAATGGAACTCCCACTTACACACTTCGA
GCTCTACAAGCAGGTTGGCATCGATCCTCCCTGAGGGGTCCTCATGTATGGCCCACCTGGCTGTGGAAAGACCATGTTAG
AAAAGGCAGTGGCACATCACATGACAGCTGCATTTATCCGTGTGGTGGGTTCAGAGTTTGTTCATAAGTACCTGGGTGAG
GGCCCCCGAATGATCTGGGATGTGTTCCTCCTGGACAAGGAGAATGCACCTGCCATCATCTTCATAGATGAAATTGATGC
CATTGCCACCAAGAGATTCGATGCCCAGACCGGAGCTGACAGGGAGGTTCAGAGGATCCTGCTGGAGCTACTGAATCAAA
TGGATGGATTTGACCAAAACATCAGTGTGAAGGCAATCATGGCCACAAACAGAACAGACACCTTGGATCCAACTCTACTT
CGGCCAGGACGCCTAGACCACAAAATTGAATTCCCACTCCCTGATCGTCACCAAAAAGAGGTTGATTTTCTCCACCATCA
CCAGCAAGATGAACCTTTCTGAGGAGGTCGACCTAGAAGACTATGTGGCCTGCCCAGATAAGATTTCAGGAGCCGATATC
AACTCCATCTGTCAGGAGACTGGAATGTTGACTGTCTGTGAGAACCGCTACATTGTCCTGGCCAAAGACTTCGAGAAAGC
ATACAAGACCGTGATCAAGAAAGATGAGCAGGAACATGAGTTTTACAAG

Alignment

ORF - retro_rnor_2414 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.65 %
• Parental protein coverage: 99.52 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EIGILVEKIQDEIPALSVSRPQTGLSFLGPEPEDLEDLYSRYKKLQQELEFLEVQEEYIKDEQKNLKKEF
          EIGILVEKIQDE.PALSVSR.QTGLSFL.PEPEDLED.YS.YKKL.QELEFLEVQEEYIKDEQKNLKKEF
Retrocopy EIGILVEKIQDEMPALSVSRLQTGLSFLQPEPEDLEDVYSLYKKL*QELEFLEVQEEYIKDEQKNLKKEF

Parental  LHAQEEVKRIQSIPLVIGQFLEAVDQNTAIVGSTTGSNYYVRILSTIDRELLKPNASVALHKHSNALVDV
          LHAQEEVK.IQSIPLVIGQFLE.VDQNT.IVGSTTGSN.YV.ILSTIDRELLKPNASV.LHKHSNALV.V
Retrocopy LHAQEEVKQIQSIPLVIGQFLEVVDQNTTIVGSTTGSNCYVCILSTIDRELLKPNASVTLHKHSNALVNV

Parental  LPPEADSSIMMLTSDQKPDVMYADIGGMDIQKQEVREAVELPLTHFELYKQIGIDPPRGVLMYGPPGCGK
          LPPEA.SSIMMLTSDQKP.VMYAD.G.MDIQKQEVREA.ELPLTHFELYKQ.GIDPP.GVLMYGPPGCGK
Retrocopy LPPEAESSIMMLTSDQKPNVMYADTGSMDIQKQEVREAMELPLTHFELYKQVGIDPP*GVLMYGPPGCGK

Parental  TMLAKAVAHHTTAAFIRVVGSEFVQKYLGEGPRMVRDVFRLAKENAPAIIFIDEIDAIATKRFDAQTGAD
          TML.KAVAHH.TAAFIRVVGSEFV.KYLGEGPRM..DVF.L.KENAPAIIFIDEIDAIATKRFDAQTGAD
Retrocopy TMLEKAVAHHMTAAFIRVVGSEFVHKYLGEGPRMIWDVFLLDKENAPAIIFIDEIDAIATKRFDAQTGAD

Parental  REVQRILLELLNQMDGFDQNVNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQ-KRLIFSTITSK
          REVQRILLELLNQMDGFDQN..VK.IMATNR.DTLDP.LLRPGRLD.KIEFPLPDR.Q.KRLIFSTITSK
Retrocopy REVQRILLELLNQMDGFDQNISVKAIMATNRTDTLDPTLLRPGRLDHKIEFPLPDRHQ>KRLIFSTITSK

Parental  MNLSEEVDLEDYVARPDKISGADINSICQESGMLAVRENRYIVLAKDFEKAYKTVIKKDEQEHEFYK
          MNLSEEVDLEDYVA.PDKISGADINSICQE.GML.V.ENRYIVLAKDFEKAYKTVIKKDEQEHEFYK
Retrocopy MNLSEEVDLEDYVACPDKISGADINSICQETGMLTVCENRYIVLAKDFEKAYKTVIKKDEQEHEFYK

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	51.98 RPM
SRP017611_kidney	0.07 RPM	62.32 RPM
SRP017611_liver	0.00 RPM	43.23 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2414 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2414 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2414 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Pteropus vampyrus	ENSPVAG00000004372	1 retrocopy	retro_pvam_227,
Rattus norvegicus	ENSRNOG00000018994	2 retrocopies	retro_rnor_1952, retro_rnor_2414 ,