RetrogeneDB ID: retro_rnor_2862

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: X:122238771..122239642(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Stip1
• Ensembl ID: ENSRNOG00000021164
• Aliases: None
• Description: Stress-induced-phosphoprotein 1 [Source:UniProtKB/Swiss-Prot;Acc:O35814]

Sequence

>retro_rnor_2862
CCCCACAAGGAGGCCAAGTCAGAACCAATGGAAGAAGATCTTCCAGAGAACAAGAAACAGGCACTGAAAGGAATGGAGTT
GGGAAATGCCTACAAGAAGAAAGATTTTGACAAGTTCCTGAAGCATTATGACAGGGCCAAGCAGCTGAACCCTATCGATA
TGACTTATATAACTCATAAAGCAGCTTTGCACTTTGAGAAGGGTGACTCCAACAAATGCCAGGAGCTCTGTGAGAAGCCA
CTGAAGTGGGCAGAGAGAACAGAAAAGACTTCCACAAGATCACCAAAGCTTATGCCCAAACTGGCAATTGCTATCTCAGA
TAAGAAAGTTACAAGGATGCTATCCATTTCTAAAACAAGTCTCTGGCAGAGCACTGAACTGCAGAAGTGCTCAAGATGTG
CCAGCAGAAAGAGAATATTCTGAAGGAATAAGAACAACTGGCTTATATCAACCCTGACTTGGCTTTGGAGGAAAAGATTA
AGAGCAATGAATGATTCCAGAAAGGGGACTAACACCAGGCCACGATGCACTATACAGAAGCCATTTGAAAAAAACCCAAG
AAGTGCCAAATGGTACAGAAACTAAGCTGCCTGCTACACCAAGATCCTGGAGTTTCAGCTGGAACTCAAGGACTGTGAAG
AGTGCATCCATCTAGAGCTAACCTTCATCAAGGGCTATACACAGAAATGATCTGCTCTGGAAGCTGTGAGGGGACTATAC
AAAAGCCATGGATATGTACCAAAAGACATTAGACCTGGACTCCAACTGTAAGGAAGCAGCAGATAGTTACCAATGATGTA
TGATGGCACAGTACAACAGGCATGATAGCCCTGAAGATGTGAAGCAGAGGGCCAGTGCTGACCCTGAGGTC

Alignment

ORF - retro_rnor_2862 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.19 %
• Parental protein coverage: 53.49 %
• Number of stop codons detected: 9
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  PKKEAKPEPMEEDLPENKKQALKEKELGNDAYKKKDFDKALKHYDKAKELDPTNMTYITNQAAVHFEKGD
          P.KEAK.EPMEEDLPENKKQALK..ELGN.AYKKKDFDK.LKHYD.AK.L.P..MTYIT..AA.HFEKGD
Retrocopy PHKEAKSEPMEEDLPENKKQALKGMELGN-AYKKKDFDKFLKHYDRAKQLNPIDMTYITHKAALHFEKGD

Parental  YNKCRELCEK-AIEVGRENREDYRQIAKAYARIGNSYFKEERYKDAIHFYNKSLAEHRTPDVLKKCQQAE
          .NKC.ELCEK.A.EVGRENR.D...I.KAYA..GN.Y...E.YKDAIHF.NKSLAEH.T..VLK.CQQ.E
Retrocopy SNKCQELCEK<ATEVGRENRKDFHKITKAYAQTGNCYLR*ESYKDAIHF*NKSLAEH*TAEVLKMCQQKE

Parental  KILKEQERLAYINPDLALEEKNKGNECFQKGDYPQAMKHYTEAI-KRNPRDAKLYSNRAACYTKLLEFQL
          .ILKE.E.LAYINPDLALEEK.K.NE.FQKGD..QA..HYTEAI...NPR.AK.Y.N.AACYTK.LEFQL
Retrocopy NILKE*EQLAYINPDLALEEKIKSNE*FQKGD*HQATMHYTEAI>EKNPRSAKWYRN*AACYTKILEFQL

Parental  ALKDCEECIQLEPTFIKGYTRKAAALEAMK-DYTKAMDVYQKALDLDSSCKEAADGYQRCMMAQYNRHDS
          .LKDCEECI.LE.TFIKGYT.K..ALEA...DYTKAMD.YQK.LDLDS.CKEAAD.YQ.CMMAQYNRHDS
Retrocopy ELKDCEECIHLELTFIKGYTQK*SALEAVR>DYTKAMDMYQKTLDLDSNCKEAADSYQ*CMMAQYNRHDS

Parental  PEDVKRRAMADPEV
          PEDVK.RA.ADPEV
Retrocopy PEDVKQRASADPEV

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	126.61 RPM
SRP017611_kidney	0.00 RPM	75.64 RPM
SRP017611_liver	0.00 RPM	38.93 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2862 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2862 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2862 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000015663	2 retrocopies	retro_btau_836, retro_btau_913,
Canis familiaris	ENSCAFG00000014672	6 retrocopies	retro_cfam_1077, retro_cfam_1172, retro_cfam_1722, retro_cfam_1982, retro_cfam_474, retro_cfam_497,
Callithrix jacchus	ENSCJAG00000018209	2 retrocopies	retro_cjac_1043, retro_cjac_2222,
Cavia porcellus	ENSCPOG00000002914	1 retrocopy	retro_cpor_1443,
Felis catus	ENSFCAG00000005937	1 retrocopy	retro_fcat_1510,
Homo sapiens	ENSG00000168439	1 retrocopy	retro_hsap_4867,
Gorilla gorilla	ENSGGOG00000012132	1 retrocopy	retro_ggor_3040,
Microcebus murinus	ENSMICG00000016933	1 retrocopy	retro_mmur_1045,
Macaca mulatta	ENSMMUG00000012953	1 retrocopy	retro_mmul_2607,
Nomascus leucogenys	ENSNLEG00000004777	1 retrocopy	retro_nleu_2000,
Pan troglodytes	ENSPTRG00000003820	1 retrocopy	retro_ptro_3242,
Rattus norvegicus	ENSRNOG00000021164	2 retrocopies	retro_rnor_2862 , retro_rnor_468,
Ictidomys tridecemlineatus	ENSSTOG00000014262	1 retrocopy	retro_itri_1578,
Tursiops truncatus	ENSTTRG00000010235	1 retrocopy	retro_ttru_1900,