RetrogeneDB ID: retro_rnor_1652

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 2:153775557..153776097(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Spryd7
• Ensembl ID: ENSRNOG00000015095
• Aliases: Spryd7, Clld6, RGD1306437
• Description: SPRY domain-containing protein 7 [Source:UniProtKB/Swiss-Prot;Acc:Q5M7T2]

Sequence

>retro_rnor_1652
TCTGGCCTCATTCCTTTCAAAGAGATGATGGCAGTACAGTTGGACATGCAGCATTGGGAAAAGATGCTGTGATTGTGAAA
AACAGAAGAAGAGTCTGTGGCACCGGAAGTTGTTTAGCCAATGCAGCCTTACATGAGAACAAAAGCTATATTGACTTCAA
AATCCAGTCTACTAGAATCTGGAGTATAGATCTTGCAACTCAGAAAGTTAACTTGAAACAGATTCCTCTTGACTGAGACA
TGCATAGCCTAGTGATGAGAAATGGCAGAGCTCTGTACCACAAAAACAAAGAGAAAAACAGGCTGCTGGCAAAATGCCTT
CCTCAGGAGGGAGACGTAGTGGCTATAACATATGATCATATAGAATTAAATGTATATTTGAATGGTGAAAACATGAATTG
TCCATCATCAGGTATACAAGGGACAATGTATCTGGTTGTGTATGTTGATGATGGTGCAATTTTGGATTGCAAGTTCTGTG
ATTTTTATCATACTCCTACAACTGATTTTTTAAAAAGCGCTATTTGAGCAGTAGCTCTTC

Alignment

ORF - retro_rnor_1652 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.98 %
• Parental protein coverage: 91.84 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TGHIPLKEMPAVQLDTQH-MGTDVVIVKNGRRICGTGGCLASAPLHQNKSYFEFKIQSTGIWGIGVATQK
          .G.IP.KEM.AVQLD.QH..G.D.VIVKN.RR.CGTG.CLA.A.LH.NKSY..FKIQST.IW.I..ATQK
Retrocopy SGLIPFKEMMAVQLDMQH<LGKDAVIVKNRRRVCGTGSCLANAALHENKSYIDFKIQSTRIWSIDLATQK

Parental  VNLNQIPLGRDMHSLVMRNDGALYHNNEEKNRLPANSLPQEGDVVGITYDHVELNVYLNGKNMHCPASGI
          VNL.QIPL..DMHSLVMRN..ALYH.N.EKNRL.A..LPQEGDVV.ITYDH.ELNVYLNG.NM.CP.SGI
Retrocopy VNLKQIPLD*DMHSLVMRNGRALYHKNKEKNRLLAKCLPQEGDVVAITYDHIELNVYLNGENMNCPSSGI

Parental  RGTVYPVVYVDDSAILDCQFSEFYHTPPPGFE-KILFEQQIF
          .GT.Y.VVYVDD.AILDC.F..FYHTP...F..K.LFEQ..F
Retrocopy QGTMYLVVYVDDGAILDCKFCDFYHTPTTDFL>KALFEQ*LF

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	18.12 RPM
SRP017611_kidney	0.00 RPM	12.21 RPM
SRP017611_liver	0.00 RPM	26.42 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1652 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1652 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1652 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000010799	2 retrocopies	retro_mdom_1497, retro_mdom_613,
Mus musculus	ENSMUSG00000021930	1 retrocopy	retro_mmus_3095,
Rattus norvegicus	ENSRNOG00000015095	1 retrocopy	retro_rnor_1652 ,
Tarsius syrichta	ENSTSYG00000007075	1 retrocopy	retro_tsyr_791,