RetrogeneDB ID: retro_rnor_468

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 1:108721061..108722680(+)
• 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_468
ATGGAGCAGGTGAATGAGCTAAAGAAGAAGGGCAATAAGGCCCTGAGTGCTGGGAACATTGAAGATGCCTTACAGTGCTA
CTCTGAGTCAATTAAACTAGATCCTCAGAACCATGTGCTCTATAGTAATCGCTCTGCAGCTTATGCCAAGAAAGGAGACT
ACCAGTAGGCCTATGAGGACAGTTGGAAGACTGTTGACCTGAAGCCTGACTGGGGCAAGGGTTATTCAAGAAAAGCAGCA
GCCCTTGAGTTCCTAAACCGGTTTGAAGAAGCCAAACGAACCTATGGAGGTTTCAAACATGAAGCCAATAATATCCAGCT
TAAGGAGGACTTGCAGAACATGGAGGCCAGGTTGGCAGAGAGGAAATTCATGAATCCTTTCAACTTGCCTAATCTGTACC
ACAAGTTAGAGAATGATCCCAGGATAAGGGCACTGCTCAGTGACCCCACCTACAGGGAACTCATAGAGCAGCTACAGAGC
AAGCCTTCAGACCTGGGCACGAAACTCCAAGATCCCCGGGTCATGACTACTCTCACTGTCCTCCTTGGGGTTGATCTGGG
CAGTGTGGATGAAAAGGAAGAGGCAGAAACACCCCCACCTCCATCCCCTTCTAAAAAGGAGGCCAAGTCAGAACCAATGG
AAGAAGATCTTCCAGAGAATAAAAAACAGGCTCTGAAAGAAAAGGAGTTGGGAAATGATGCCTACAAGAAGAAAGATTTT
AACAAGGCCCAGAAGCATTATGACAGGGCCAAGGAGCTGAACCTACCAGTATGACTTACAGAACTAATCAGGCAGCTGTG
CACTTTGAGAAGGGCGACTACAACAAATGCCGGGAGCTCTGTGAGAAGGCCATTGAAGTAGGCAGATAGAACGGAGAGGA
CTACCGACAGTTCGCCAAAGCTTATGCCTGAATTGGCAATTCCTATTTCAAAGAAGAAAGGTACAAGGATGATATCCATT
TCTACAAGTCTCTGGCAGAGCACCGAAACCCAGATGTACTCAAGAAAGGCCAACAGGCAGAGAAAATTCTGAAGAAACAA
GAGTGTCAGGCTTATATCAACCCTGACTTGGCTTTGGAGGAAAAGAATAAGGGCAATGAGTGCTTCCAGAAAGGGGACTA
CCCCCAGGCCATGAAGCACTATACAGAAGCCATTAAAAGGAACCCAAGAGATGCCAAACTATAGAGCAACCAAGCTACCA
GCTACACCAAGCTCCTGGAGTTTCACTTGGCACTCAAGGACTGTGAAGAGTGCATCCAGCTAGAGCCAAACTTCATCAAG
GGTTATACCTGGAAATCAGCTGCTCTGGAAGTCATGAAGGACTACACGAAAGCCATGGATGTGTATCAGAAGGCGCTAGA
CCTGGACTCCAGCTGTAAGGAAGCAGCAGATGGTTCCAACTATATGATGGCACAGTACAACAGACACGGTAGCCCTGAGC
ATGTGAAGCAGCGGGCCATGGCTGATCCTGAGGTGCAGCAGTTATTGAGGGACCCAGCCATGAGGCTCATCCTGGAGCAG
ATACAAAAGGACCCCTCCAGGCTCTGAGCGAACACTTAGAATCCTGTAATAGCACAGAAGATCCAGAAGTCGATGGTTGT
GGGTCTGATCGCAATTCGG

Alignment

ORF - retro_rnor_468 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.13 %
• Parental protein coverage: 99.82 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VEQVNELKEKGNKALSAGNIDDALQCYSEAIKLDPQNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLKPD
          .EQVNELK.KGNKALSAGNI.DALQCYSE.IKLDPQNHVLYSNRSAAYAKKGDYQ.AYED..KTVDLKPD
Retrocopy MEQVNELKKKGNKALSAGNIEDALQCYSESIKLDPQNHVLYSNRSAAYAKKGDYQ*AYEDSWKTVDLKPD

Parental  WGKGYSRKAAALEFLNRFEEAKRTYEEGLKHEANNLQLKEGLQNMEARLAERKFMNPFNLPNLYQKLEND
          WGKGYSRKAAALEFLNRFEEAKRTY..G.KHEANN.QLKE.LQNMEARLAERKFMNPFNLPNLY.KLEND
Retrocopy WGKGYSRKAAALEFLNRFEEAKRTYG-GFKHEANNIQLKEDLQNMEARLAERKFMNPFNLPNLYHKLEND

Parental  PRTRTLLSDPTYRELIEQLQNKPSDLGTKLQDPRVMTTLSVLLGVDLGSMDEEEEAATPPPPPPPKKEAK
          PR.R.LLSDPTYRELIEQLQ.KPSDLGTKLQDPRVMTTL.VLLGVDLGS.DE.EEA.TPPPP.P.KKEAK
Retrocopy PRIRALLSDPTYRELIEQLQSKPSDLGTKLQDPRVMTTLTVLLGVDLGSVDEKEEAETPPPPSPSKKEAK

Parental  PEPMEEDLPENKKQALKEKELGNDAYKKKDFDKALKHYDKAKEL-DPTNMTYITNQAAVHFEKGDYNKCR
          .EPMEEDLPENKKQALKEKELGNDAYKKKDF.KA.KHYD.AKEL..PT.MTY.TNQAAVHFEKGDYNKCR
Retrocopy SEPMEEDLPENKKQALKEKELGNDAYKKKDFNKAQKHYDRAKEL<EPTSMTYRTNQAAVHFEKGDYNKCR

Parental  ELCEKAIEVGRENREDYRQIAKAYARIGNSYFKEERYKDAIHFYNKSLAEHRTPDVLKKCQQAEKILKEQ
          ELCEKAIEVGR.N.EDYRQ.AKAYA.IGNSYFKEERYKD.IHFY.KSLAEHR.PDVLKK.QQAEKILK.Q
Retrocopy ELCEKAIEVGR*NGEDYRQFAKAYA*IGNSYFKEERYKDDIHFY-KSLAEHRNPDVLKKGQQAEKILKKQ

Parental  ERLAYINPDLALEEKNKGNECFQKGDYPQAMKHYTEAIKRNPRDAKLYSNRAACYTKLLEFQLALKDCEE
          E..AYINPDLALEEKNKGNECFQKGDYPQAMKHYTEAIKRNPRDAKL.SN.A..YTKLLEF.LALKDCEE
Retrocopy ECQAYINPDLALEEKNKGNECFQKGDYPQAMKHYTEAIKRNPRDAKL*SNQATSYTKLLEFHLALKDCEE

Parental  CIQLEPTFIKGYTRKAAALEAMKDYTKAMDVYQKALDLDSSCKEAADGYQRCMMAQYNRHDSPEDVKRRA
          CIQLEP.FIKGYT.K.AALE.MKDYTKAMDVYQKALDLDSSCKEAADG....MMAQYNRH.SPE.VK.RA
Retrocopy CIQLEPNFIKGYTWKSAALEVMKDYTKAMDVYQKALDLDSSCKEAADG-SNYMMAQYNRHGSPEHVKQRA

Parental  MADPEVQQIMSDPAMRLILEQMQKDPQALSEHLKNPVIAQKIQKLMDVGLIAIR
          MADPEVQQ...DPAMRLILEQ.QKDP..L.....NPVIAQKIQK.M.VGLIAIR
Retrocopy MADPEVQQLLRDPAMRLILEQIQKDPSRL*ANT*NPVIAQKIQKSMVVGLIAIR

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	0.14 RPM	126.61 RPM
SRP017611_kidney	0.21 RPM	75.64 RPM
SRP017611_liver	0.07 RPM	38.93 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_468 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_468 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_468 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,