RetrogeneDB ID: retro_rnor_2916

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: X:43571168..43572142(-)
• Located in intron of: ENSRNOG00000048840

Retrocopy information

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

Parental gene information

• Parental gene symbol: Sqstm1
• Ensembl ID: ENSRNOG00000003147
• Aliases: Sqstm1, Osi, ZIP, ZIP3
• Description: Sequestosome-1 [Source:UniProtKB/Swiss-Prot;Acc:O08623]

Sequence

>retro_rnor_2916
GATGAGGATGGGGACTTGGTTGCCTTTTCCAGTGATGAGGAGCTGACAATGACCATGTCCTACGTTAAAGATGACATCTT
CTGCATCTACATTAAAGAGAAGAAGGAATGCTGGCAGGATCATCACCCACCATGTGCTCAGAATGCCCGAAGCATGGTGC
ACCCCAATGTGATTTGTGAAGGTTGCAACGGGCCTGTGGTGGGAATTCGCTCTAAGTTCAGTGTGTGCCCAGACAACAAC
CTGTGCAGAGTCTGCGAGGGGAAGGGCCTGCACAGGGAGCACAGCAAGCTCATCTTTCCCAACCCCTTTGGCCACCTCTC
TGATAGCTTCTCTCATAGCCGCTGGCTTCGGAAGCTGAAACATGGACACTTTGGCTGGCCTGGCTAAAAGATGGGTCCAT
CAGGGAACTGGAACCCAGGTCCTCCTCAAGCAGGGGATGGTCGCCCTTGCCCCACAGCAGAGTCAGGCATTGAAGCTGAC
ATTAATGTGGAACATGGAGGGAGGGGAAGCCACCTGACACCCACCTCCCCAGAAAGTTCCAGCACAAGCACAGAAGACAA
GAGTGCCACTCAGCCAAGCAGCTGTTCCTTGGAAGTCAGCAAACCTGACAGGGCCGGGGAGGAGCATGCTCAGGCTCTGA
CAGAGCAGATGAAGAAGATAGCCTTGGAGTCGGTGGGACAGCCAGAGGAACAAATGGAGTCAGGTAACTGCTCAGGAGGA
GATGACGACTGGACACATTTATCTTCAAAAGAAGTGGACCCACCCACAGGTGAACTCCAGTCTCTACAGATGCCAGAATT
GGAAGGGACAAGCTCTCTAGACTCTCACAGGAAGGACCCACAGGGCTGAAGGGAGCTACCCTGAACCCTTATCTCCCACC
AGAGACTGATCTCAGGCTGATTGAGTCACTCTCCCAGATGCTGTCCATGGGTTTCTCAGATGAAGGCAGGCGGCTGGCTC
AGCAGGTTCCTACA

Alignment

ORF - retro_rnor_2916 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.74 %
• Parental protein coverage: 78.88 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DEDGDLVAFSSDEELTMAMSYVKDDIFRIYIKEKKECRREHRPPCAQEARSMVHPNVICDGCNGPVVGTR
          DEDGDLVAFSSDEELTM.MSYVKDDIF.IYIKEKKEC...H.PPCAQ.ARSMVHPNVIC.GCNGPVVG.R
Retrocopy DEDGDLVAFSSDEELTMTMSYVKDDIFCIYIKEKKECWQDHHPPCAQNARSMVHPNVICEGCNGPVVGIR

Parental  YKCSVCPDYDLCSVCEGKGLHREHSKLIFPNPFGHLSDSFSHSRWLRKLKHGHFGWPGWEMGPPGNWSPR
          .K.SVCPD..LC.VCEGKGLHREHSKLIFPNPFGHLSDSFSHSRWLRKLKHGHFGWPG..MGP.GNW.P.
Retrocopy SKFSVCPDNNLCRVCEGKGLHREHSKLIFPNPFGHLSDSFSHSRWLRKLKHGHFGWPG*KMGPSGNWNPG

Parental  PPRAGDGRPCPTAESGIEVDIDVEHGGKRSRLTPTSAESSSTGTEDKSGTQPSSCSSEVSKPDGAGEGPA
          PP.AGDGRPCPTAESGIE.DI.VEHGG..S.LTPTS.ESSST.TEDKS.TQPSSCS.EVSKPD.AGE..A
Retrocopy PPQAGDGRPCPTAESGIEADINVEHGGRGSHLTPTSPESSSTSTEDKSATQPSSCSLEVSKPDRAGEEHA

Parental  QSLTEQMKKIALESVGQPEELMESDNCSGGDDDWTHLSSKEVDPSTGELQSLQMPESEGPSSLDP-SQEG
          Q.LTEQMKKIALESVGQPEE.MES.NCSGGDDDWTHLSSKEVDP.TGELQSLQMPE.EG.SSLD..SQEG
Retrocopy QALTEQMKKIALESVGQPEEQMESGNCSGGDDDWTHLSSKEVDPPTGELQSLQMPELEGTSSLDS<SQEG

Parental  PTGLKEAALYPHLPPEADPRLIESLSQMLSMGFSDEGGWLTRLLQT
          PTGLK.A.L.P.LPPE.D.RLIESLSQMLSMGFSDEG..L.....T
Retrocopy PTGLKGATLNPYLPPETDLRLIESLSQMLSMGFSDEGRRLAQQVPT

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	327.27 RPM
SRP017611_kidney	0.00 RPM	265.80 RPM
SRP017611_liver	0.00 RPM	266.93 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2916 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2916 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2916 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000003806	1 retrocopy	retro_mdom_1849,
Nomascus leucogenys	ENSNLEG00000007969	1 retrocopy	retro_nleu_703,
Rattus norvegicus	ENSRNOG00000003147	1 retrocopy	retro_rnor_2916 ,