RetrogeneDB ID: retro_rnor_1750

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 20:1326059..1327471(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Sppl2a
• Ensembl ID: ENSRNOG00000011652
• Aliases: Sppl2a, RGD1563001
• Description: signal peptide peptidase-like 2A precursor [Source:RefSeq peptide;Acc:NP_001101240]

Sequence

>retro_rnor_1750
ATGGAGCTGCTGCATTAGCTGCAAGCTCCCGCTGCTGCCCTGCTCTGGAGCTGCCTCATTGAACTGACAGCTGCTCAGGA
AGCTATCCTTCTGTGTCTGCAAATTATGTATCTTCACTTTCCAAGGACTGCTGCATGAATTTTAACAACAACTGGATGCA
GCTTCCAAGTTCCCTAGAAAATGCAACTTCTCTTAGCTTGATGACTCTGACTGGCACAACACTGTGCCATCGTTCTGATA
TTACTCTTGATGGCATAAAGAACAAGTCAGTGGTGATGCACTGGGGACCCTGCCATTTACTTGAAAAAGCCAAAATTGCA
CAAGAAGGTGGTGCTGCAGCGTTGCTGGTTGCCAACAACAGTGTCCTAATTCCTTCCTCAAGGAACAAATATGCATTATG
AAATGTAACTATACTAATAGCAGTTATAACCCAAAAAGACTTTAAAGATATGAAAGAGACTCTTGGAGATGATATTACCG
TGACAATGTATTCTCTATCCTGACCTAACTTTGACTATACCCTGGTGGTCATTTTGGTAATTGCTATGTTCACTGTGGCA
TTAGGAGGATACTGGAGTGGACTTATTGAATTGGAAAACATGAAGGGAGTGGAAGATGCTAAAGACAGAGAGACAAATAG
AAAGAAGGAAGATTACTTAACATTCAGTCTTCACATGGTTGCCGTGTTCATGGTCATGTGCTGTGTAATGATTGTCTTAC
TGTATTTCTTCTACAGGCGGCTCGTTGTATGTTATGATAGCAGTTTTCTGCATAGCGTCAGCAATGAGCCTGTACAACTG
TCTTGCTGCACTGATTCATAGGGTGCCATGTGGACAGTGCGCAGTGTTGTGTTGTGGCAAAAGCATTAAAGGGAGCCTGA
TTTCCCTTTCTGGACTGTGCATCTCAGTTGCTGTTGTGTGGGCTGTGCTTCGAAAAGAGGATAGGTGGGCTTGGATTTTA
CAGAATGTCTTCGGAACTGCTTTCTGTCTCTACTTAATTAAAACAATGAAGTTACCCAATTTCATGTCATGTGTGATACT
GCTAGGCCTTCTCCTCATCTATGATGTGTTCTTTGTCTTCATAACACCCTTCATCACAACATAGGGAGAGAACGTCATGG
TGGAACTTGCTGCTGGGCCTTCCGAGAATGCTGAGAAGTTGCCAGTAGTTATCAGGGTGACAAAACTGATGGGTTATTCA
CTCATGGGTGTATGCTCAGTGCCTGTTTCAGTATTGGGTTTCGGAGATATCATTCTACCAGGTCTGTTGATTGCATATTG
TAAAAGATTTGATGTTCAGACGGGTTCTTCTCTATACTGTATTTCATCCACAATTGCCTATGCTGCTGGCATGGTAATTA
CATTTGTTCTCCTAATGCTGAGGAAGACGGACAGCCTGCTCTCCTCTATTTA

Alignment

ORF - retro_rnor_1750 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.49 %
• Parental protein coverage: 90.06 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MGLLHSLHAPAAALLWSCLLGLSAAQEAIL-HASANGVSSLSKDYCMYYNNNWTRLPSSLENATSLSLMN
          M.LLH.L.APAAALLWSCL..L.AAQEAIL...SAN.VSSLSKD.CM..NNNW..LPSSLENATSLSLM.
Retrocopy MELLH*LQAPAAALLWSCLIELTAAQEAIL<SVSANYVSSLSKDCCMNFNNNWMQLPSSLENATSLSLMT

Parental  LTGTPLCHLSDIPPDGIKNKAVVVHWGPCHFLEKAKIAQEGGAAALLIANNSVLIPSSRNKSAFQNVTIL
          LTGT.LCH.SDI..DGIKNK.VV.HWGPCH.LEKAKIAQEGGAAALL.ANNSVLIPSSRNK.A..NVTIL
Retrocopy LTGTTLCHRSDITLDGIKNKSVVMHWGPCHLLEKAKIAQEGGAAALLVANNSVLIPSSRNKYAL*NVTIL

Parental  IAVITQKDFNDMKETLGDDITVKMYSPSWPNFDYTLVVIFVIAVFTVALGGYWSGLIELESMKAVEDAED
          IAVITQKDF.DMKETLGDDITV.MYS.S.PNFDYTLVVI.VIA.FTVALGGYWSGLIELE.MK.VEDA.D
Retrocopy IAVITQKDFKDMKETLGDDITVTMYSLS*PNFDYTLVVILVIAMFTVALGGYWSGLIELENMKGVEDAKD

Parental  REARKKKEDYLTFSPLTVVLFVVICCVMIVLLYFFYKWLV-YVMIAIFCIASATSLYNCLAALIHRMPCG
          RE...KKEDYLTFS...V..F.V.CCVMIVLLYFFY..LV.YVMIA.FCIASA.SLYNCLAALIHR.PCG
Retrocopy RETNRKKEDYLTFSLHMVAVFMVMCCVMIVLLYFFYRRLV>YVMIAVFCIASAMSLYNCLAALIHRVPCG

Parental  QCTILCCGKNIKVSLIFLSGLCISVAVVWAVFRNEDRWAWILQDILGIAFCLNLIKTMKLPNFMSCVILL
          QC..LCCGK.IK.SLI.LSGLCISVAVVWAV.R.EDRWAWILQ...G.AFCL.LIKTMKLPNFMSCVILL
Retrocopy QCAVLCCGKSIKGSLISLSGLCISVAVVWAVLRKEDRWAWILQNVFGTAFCLYLIKTMKLPNFMSCVILL

Parental  GLLLIYDVFFVFITPFITKNGESIMVELAAGPFENAEKLPVVIRVPKLMDYSVMSVCSVPVSVLGFGDII
          GLLLIYDVFFVFITPFIT..GE..MVELAAGP.ENAEKLPVVIRV.KLM.YS.M.VCSVPVSVLGFGDII
Retrocopy GLLLIYDVFFVFITPFITT*GENVMVELAAGPSENAEKLPVVIRVTKLMGYSLMGVCSVPVSVLGFGDII

Parental  VPGLLIAYCRRFDVQTGSSIYYISSTIAYAVGMIITFVVLMVMKT-GQPALLYL
          .PGLLIAYC.RFDVQTGSS.Y.ISSTIAYA.GM.ITFV.LM..KT.GQPALLYL
Retrocopy LPGLLIAYCKRFDVQTGSSLYCISSTIAYAAGMVITFVLLMLRKT<GQPALLYL

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	22.29 RPM
SRP017611_kidney	0.00 RPM	58.48 RPM
SRP017611_liver	0.00 RPM	69.39 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1750 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1750 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1750 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000008946	1 retrocopy	retro_dord_754,
Homo sapiens	ENSG00000138600	1 retrocopy	retro_hsap_1566,
Gorilla gorilla	ENSGGOG00000013154	1 retrocopy	retro_ggor_1191,
Pongo abelii	ENSPPYG00000006472	1 retrocopy	retro_pabe_1293,
Pan troglodytes	ENSPTRG00000007070	1 retrocopy	retro_ptro_1054,
Rattus norvegicus	ENSRNOG00000001178	1 retrocopy	retro_rnor_2157,
Rattus norvegicus	ENSRNOG00000011652	1 retrocopy	retro_rnor_1750 ,