RetrogeneDB ID: retro_cfam_1077

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 22:36686332..36687682(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: STIP1
• Ensembl ID: ENSCAFG00000014672
• Aliases: None
• Description: stress-induced-phosphoprotein 1 [Source:HGNC Symbol;Acc:11387]

Sequence

>retro_cfam_1077
AAGAAAGGTGACTACCAGAAGGCTTATGAGGATGGCTGCAAAACCGTTGACTTAAAGCCTGACTGGGGAAATTCGTGCTA
TTAGTGGAAAGCAGCAGCTCTCAAGTTCTTAAATTGATTTGAAAAAGCCTAACAAACCTACAAATATGGTTTAAAACATG
AAGTAAATAATCCTCACCTCAAAGAGAGCTTACAGAATATGGAGGCCCAGTTGGTAGCACAGAAATACATGAATCCTTTT
AACATGCCCAATCTATACCAGAACTTGGAGAGTGATCCCAGGACAAGAACACTGTTCTCTGGTCCTACCTTCTGGAGGGT
GAGAGAGCAACTAGGAAACAAGCCATCTGACCTCAGCACAAAACCGCAAGATCCCCAGATCAAGACTACTCTCAGTGTCC
TGTTGGGAGTCGAGCTGGACAATATGGATGAGGAGGAAGTTGGAACACCTCCCCCACCTTCTCCTCCTAAGAAAGACACC
AAGCCAGAGCCAATGGAAGAAGATATTCCAGAGAATAAGAAGTAAGTGCTGAAAGAGAAAGAGTTGGGGAATGAGGCCTA
CAAAAAGATGGACTTTGACACAGCCTTGAAGCACCATGACAGAGCCAAGGACCTGGACTTCACAACGTGACTTATATGAC
CAATCAAGTAGCCATGTACTTCGAGAAGGGCGACTACAGTAAATGCTGGGAGCTTTGTGAGAAGGCCATCGAAGTGGGGC
GAGAAAACCGAGAAGACTATTGACAGATTGCCAAAACTTATGCTCAAATTGGCAACTCCTACTTCAAAGAAGGAAAGTAC
AAGGATGCCATCCATTCCTATAACAAGTCTTTGGCAGAGCACTGAACCCCAGATGTGCTCAAGACATGTCAACAGGTGGA
GAAAATTCTGAAAGAGCAAGAGTGGCTGGCCTATATAAACCCCAACCTGGCCTTAGAGGAGAAGAACAAAGCCAAGGTAT
ATTCTCAGAAAGGGGACTATTCCCAGTTCATGAAGTATTATACAGATGCCATCAAACTGAATCCAAAAGATGCCAAATTG
TACAGCAATCGAGCTGCCAGCTACAACAAACTCCTGGAGTTTCAGCAGCGCTCAAGGATTGTGAGGAAAATATCCAGCTA
GAGTCAACCTTCATCAAGGGTTACACACAGAAAGCAGGTCACTGGAAGCAATGAAGGACTACACAAAAGCCATGGACGTC
TAACAGAAGGTGTTAGATTTGGACTCCAAGTGTAAGGAGGTGACAGACAGCTACCAAGTCTGTATGATGTCCCAGTACAA
GTGTCATGATAGCCCCAAAGGTGTGAAGTGAAGGGCCATGGCCAACCTTGAGGTGTAGTAGATAATGAGT

Alignment

ORF - retro_cfam_1077 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.12 %
• Parental protein coverage: 83.12 %
• Number of stop codons detected: 10
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KKGDYQKAYEDGCKTVDLKPDWGKG-YSRKAAALEFLNRFEEAKRTYEEGLKHEANNPQLKEGLQNMEAR
          KKGDYQKAYEDGCKTVDLKPDWG...Y..KAAAL.FLN.FE.A..TY..GLKHE.NNP.LKE.LQNMEA.
Retrocopy KKGDYQKAYEDGCKTVDLKPDWGNSCY*WKAAALKFLN*FEKA*QTYKYGLKHEVNNPHLKESLQNMEAQ

Parental  LAGTERKFMNPFNMPNLYQKLESDPRTRTLLADPTYRELIEQLRNKPSDLGTKLQDPRIMTTLSVLLGVD
          L.....K.MNPFNMPNLYQ.LESDPRTRTL...PT.....EQL.NKPSDL.TK.QDP.I.TTLSVLLGV.
Retrocopy LVA--QKYMNPFNMPNLYQNLESDPRTRTLFSGPTFWRVREQLGNKPSDLSTKPQDPQIKTTLSVLLGVE

Parental  LGSMDEEEEVGTPPPPPPPKKDTKPEPMEEDLPENKKQALKEKELGNEAYKKKDFDTALKHYDRAKDLDP
          L..MDEEE.VGTPPPP.PPKKDTKPEPMEED.PENKK..LKEKELGNEAYKK.DFDTALKH.DRAKDLD.
Retrocopy LDNMDEEE-VGTPPPPSPPKKDTKPEPMEEDIPENKK*VLKEKELGNEAYKKMDFDTALKHHDRAKDLDF

Parental  T-NMTYMTNQAAVYFEKGDYSKCRELCEKAIEVGRENREDYRQIAKAYARIGNSYFKEEKYKDAIHFYNK
          T.N.TYMTNQ.A.YFEKGDYSKC.ELCEKAIEVGRENREDY.QIAK.YA.IGNSYFKE.KYKDAIH.YNK
Retrocopy T<NVTYMTNQVAMYFEKGDYSKCWELCEKAIEVGRENREDY*QIAKTYAQIGNSYFKEGKYKDAIHSYNK

Parental  SLAEHRTPDVLKKCQQAEKILKEQERLAYINPDLALEEKNKGNECFQKGDYPQAMKHYTEAIKRNPKDAK
          SLAEH.TPDVLK.CQQ.EKILKEQE.LAYINP.LALEEKNK.....QKGDY.Q.MK.YT.AIK.NPKDAK
Retrocopy SLAEH*TPDVLKTCQQVEKILKEQEWLAYINPNLALEEKNKAKVYSQKGDYSQFMKYYTDAIKLNPKDAK

Parental  LYSNRAACYTKLLEFQ-LALKDCEECIQLEPAFIKGYTRKAA-ALEAMKDYTKAMDVYQKALDLDSNCKE
          LYSNRAA.Y.KLLEFQ..ALKDCEE.IQLE..FIKGYT.KA...LEAMKDYTKAMDV.QK.LDLDS.CKE
Retrocopy LYSNRAASYNKLLEFQ<AALKDCEENIQLESTFIKGYTQKAG<SLEAMKDYTKAMDV*QKVLDLDSKCKE

Parental  AADGYQRCMMAQYNRHDSPEDVKRRAMADPEVQQIMS
          ..D.YQ.CMM.QY..HDSP..VK.RAMA..EV..IMS
Retrocopy VTDSYQVCMMSQYKCHDSPKGVK*RAMANLEV**IMS

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
SRP012049_cerebellum	0.00 RPM	101.39 RPM
SRP017611_brain	0.00 RPM	99.08 RPM
SRP017611_kidney	0.00 RPM	53.82 RPM
SRP017611_liver	0.00 RPM	29.88 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1077 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1077 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1077 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,