RetrogeneDB ID: retro_rnor_2547

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 8:5102640..5103410(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Tial1
• Ensembl ID: ENSRNOG00000020271
• Aliases: None
• Description: nucleolysin TIAR [Source:RefSeq peptide;Acc:NP_001013211]

Sequence

>retro_rnor_2547
GGACTCTATACGGATGCCAGGGTAGTTAAAGATGTGGCAACTGGAAAGTCCAAAGGCTATGGTTTTGTATCTTTTTATGA
GAAACTCGATGCAGAGAATGCAGTTGTGCATATTTGAGGTGGGGGTTGTCAGTGGCTGGGAGGTTGACAAATCAGAACCA
GTTGGGCCACACGTAAACCACCTGCCCCTAACGTACACAAGAAACTAATACTAAGCAGTTGAGATTTGAAGATGGAGTAA
ACCAGTCAAGTACAAAAAAACTACACTGTGTAAGGTGGAGGAATTGCTTCGGGGCTGACAGAACAATTTGTGAGACAAAT
ATTTTCACCATTGGACAAACTATGGAAATAAGTTTTTCCAGAGAAGGGCTATTTGTTTGTTAGATTTTCAACGTATGAAC
GTGCAGCCCATGCCATTGTTTCTGTGAACCGTACTACAATCGAAGGACATGTGAGTAAATGTTATTGGGGTGAAGAATCT
CCTGATATGACTGAAAACTTCCAACAGGTTGACGACGTCAGTGGGGCCAGTGCAGCCAAGTGTACGGAAACACACAAGGG
TTCGGCAAGCATATGGCAAACGGGTGCCAGGTGCCTCCTTGTGGCGTCTATGTGCAGCCATGGAACCAACAAGGATTGGC
AGTAGATCAATCACCATCTGCTGCTTCGATGGGTGGTTTTGCTGCTCGGCCTCCTGAAAGACAAGTTCCTCCCCCTGTAA
TACCTTCTCCAAACCAAGCTGAGTAGGGAATGGCAAGTTTCCCAGCACAA

Alignment

ORF - retro_rnor_2547 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.1 %
• Parental protein coverage: 65.05 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM---GGQWLGGRQIRTNWATRKPPAPK-STQET
          G...DARVVKD.ATGKSKGYGFVSFY.KLDAENA.VH....G.QWLGG.QIRT.WATRKPPAP...TQET
Retrocopy GLYTDARVVKDVATGKSKGYGFVSFYEKLDAENAVVHI*GGGCQWLGG*QIRTSWATRKPPAPN<RTQET

Parental  NTKQLRFEDVVNQSSPK-NCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKGYSFVRFSTHESAAH
          NTKQLRFED.VNQSS.K.N.TV..GGIASGLT.Q..RQ.FSP........VFPEKGY.FVRFST.E.AAH
Retrocopy NTKQLRFEDGVNQSSTK>NYTV*GGGIASGLTEQFVRQIFSPLDKLWK*-VFPEKGYLFVRFSTYERAAH

Parental  AIVSVNGTTIEGHVVKCYWGKESPDMTKNFQQVD-YSQWGQWSQVYGNPQQYGQYMANGWQVPPYGVYGQ
          AIVSVN.TTIEGHV.KCYWG.ESPDMT.NFQQVD...QWGQ.SQVYGN.Q..G..MANG.QVPP.GVY.Q
Retrocopy AIVSVNRTTIEGHVSKCYWGEESPDMTENFQQVD<RRQWGQCSQVYGNTQGFGKHMANGCQVPPCGVYVQ

Parental  PWNQQGFGVDQSPSAAWMGGFGAQPPQGQAPPPVIPPPNQAGYGMASFPTQ
          PWNQQG..VDQSPSAA.MGGF.A.PP..Q.PPPVIP.PNQA..GMASFP.Q
Retrocopy PWNQQGLAVDQSPSAASMGGFAARPPERQVPPPVIPSPNQAE*GMASFPAQ

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	50.90 RPM
SRP017611_kidney	0.00 RPM	30.22 RPM
SRP017611_liver	0.00 RPM	26.49 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2547 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2547 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2547 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
Choloepus hoffmanni	ENSCHOG00000009888	2 retrocopies	retro_chof_2395, retro_chof_670,
Oryctolagus cuniculus	ENSOCUG00000003783	1 retrocopy	retro_ocun_904,
Rattus norvegicus	ENSRNOG00000020271	1 retrocopy	retro_rnor_2547 ,
Sus scrofa	ENSSSCG00000010685	1 retrocopy	retro_sscr_11,