RetrogeneDB ID: retro_cfam_474

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 12:972870..974498(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000000496
• Aliases: None
• Status: KNOWN_PSEUDOGENE

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_474
ATAGAGCAGGTAAATGAGCTGAAAGAGAAGGGCAATAAGGCCCTGAGTGCGGGCAACATTGATGACGCACTGCAGTGCTA
CTCTGAGGCCATTAAGTTAGATCCCCAGAACCATGTGCTCTATAGCAATCGCTCTGCAGCTTACGCCAAGAAAGGGGACT
ACCAGAAGGCTTATGAGGATGGCTGCAAAACGGTGGACTTAAAGCCCGACTGGGGCAGGGGCTATTCGAGGAAGGCTGCA
GCCCTTGAGTTCTTAAACCGATTTGAAGAAGCCAAGCGAACCTACGAAGAGGGTTTAAAACATGAAGCAAATAATCCTCA
GCTCAAAGAGGGCTTACAGAATATGGAGGCTCGGTTGGCAGAACGGAAATTCATGAACCCTTTCAACATGCCCAATCTGT
ACCAGAAATTGGAGAGTGATCCCAGGACAAGGACACTGCTCGCTGATCCTACCTACCGGGAGCTGATAGAGCAACTACGA
AACAAGCCATCTGACTTGGGCACGAAACTGCAAGATCCCCGGATCATGACTACTCTGAGCATCCTGCTGGGTGTGGATCT
GGGCAGTATGGATGAGGAGGAGGAAGTTGGAACACCTCCCCCACCTCCTCCTCCCAGGAAGGACACCAAGCCAGAGGCAA
TGGAAGAAGATCTTCCAGAGAATAAGAAGCAGGCGCTGAAAGAGAAAGAGCTGGGGAATGAAGCCTACAAGAAGAAAGAC
TTTGACACAGCCTTGAAGCACTATGACAGAGCCAAGGACCTGGACCCCACCAACATGACTTACTTGACCAATCAAGCAGC
CGTGTACTTCGAGAAGGGCGACTACAGTAAATGCCGGGAGCTTTGTGAGAAGGCCATCGAAGTGGGGCGAGAAAACCGAG
AAGACTATCGACAGATTGCCAAAGCTTATGCTCGAATTGGCAACTCCTACTCCAAGGAAGAAAAGTGCAAGGCTACCACC
CATTTCTATAACAAGTCTTTGGCAGAGCACCGGACCCCAGATGTGCTCAAGAAATGCCAACAGGCAGAGAAAATTCTGAA
GGAGCAAGAGCGGCTGGCTTACATAAACCCAGATCTGGCCTTGGAGGAGAAGAACAAAGGCAATGAATGTTTTCAGAAAG
GGGACTATCCCCAGGCCATGAAGCATTATACAGAAGCCATCAAACGGAATCCAAAAGATGCCAAATTGTACAGCAATCGA
GCTGCCTGCTACACCAAACTCCTGGAGTTTCAGCTGGCGCTCAGGACTGTGAGGAATGTATCCAGCTAGAGCCGGCCTTC
ATCAAGGGGTACACCCGGAAAGCAGCTGCCCTGGAGGCAATGAAGGACTACACGAAAGCCATGGATGTCTACCAGAAGGC
GTTAGATCTGGACTCCACCTGCAAGGAAGCGGCAGACGGTTACCAGCGCTGTATGATGGCCCAGTACAACCACCACGATA
ACCCCGAAGACGTGAAGCGACGGGCCATGGCTGACCCTGAGGTGCAGCAGATAATGAGTGACCCTGCCACGCGGCTTATC
CTGGAGCAGATGCAGAAGGACCCTCAGGCACTCAGCGAACACTTAAAGAATCCTGTAATAGCCCAGAAGATCCAGAAGCT
GACGGATGTGGGTCTGATTGCAATTCGG

Alignment

ORF - retro_cfam_474 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.34 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IKQVNELKEKGNKALSAGNIDDALQCYSEAIKLDPQNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLKPD
          I.QVNELKEKGNKALSAGNIDDALQCYSEAIKLDPQNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLKPD
Retrocopy IEQVNELKEKGNKALSAGNIDDALQCYSEAIKLDPQNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLKPD

Parental  WGKGYSRKAAALEFLNRFEEAKRTYEEGLKHEANNPQLKEGLQNMEARLAGTERKFMNPFNMPNLYQKLE
          WG.GYSRKAAALEFLNRFEEAKRTYEEGLKHEANNPQLKEGLQNMEARLA..ERKFMNPFNMPNLYQKLE
Retrocopy WGRGYSRKAAALEFLNRFEEAKRTYEEGLKHEANNPQLKEGLQNMEARLA--ERKFMNPFNMPNLYQKLE

Parental  SDPRTRTLLADPTYRELIEQLRNKPSDLGTKLQDPRIMTTLSVLLGVDLGSMDEEEEVGTPPPPPPPKKD
          SDPRTRTLLADPTYRELIEQLRNKPSDLGTKLQDPRIMTTLS.LLGVDLGSMDEEEEVGTPPPPPPP.KD
Retrocopy SDPRTRTLLADPTYRELIEQLRNKPSDLGTKLQDPRIMTTLSILLGVDLGSMDEEEEVGTPPPPPPPRKD

Parental  TKPEPMEEDLPENKKQALKEKELGNEAYKKKDFDTALKHYDRAKDLDPTNMTYMTNQAAVYFEKGDYSKC
          TKPE.MEEDLPENKKQALKEKELGNEAYKKKDFDTALKHYDRAKDLDPTNMTY.TNQAAVYFEKGDYSKC
Retrocopy TKPEAMEEDLPENKKQALKEKELGNEAYKKKDFDTALKHYDRAKDLDPTNMTYLTNQAAVYFEKGDYSKC

Parental  RELCEKAIEVGRENREDYRQIAKAYARIGNSYFKEEKYKDAIHFYNKSLAEHRTPDVLKKCQQAEKILKE
          RELCEKAIEVGRENREDYRQIAKAYARIGNSY.KEEK.K...HFYNKSLAEHRTPDVLKKCQQAEKILKE
Retrocopy RELCEKAIEVGRENREDYRQIAKAYARIGNSYSKEEKCKATTHFYNKSLAEHRTPDVLKKCQQAEKILKE

Parental  QERLAYINPDLALEEKNKGNECFQKGDYPQAMKHYTEAIKRNPKDAKLYSNRAACYTKLLEFQLALK-DC
          QERLAYINPDLALEEKNKGNECFQKGDYPQAMKHYTEAIKRNPKDAKLYSNRAACYTKLLEFQLAL..DC
Retrocopy QERLAYINPDLALEEKNKGNECFQKGDYPQAMKHYTEAIKRNPKDAKLYSNRAACYTKLLEFQLALR<DC

Parental  EECIQLEPAFIKGYTRKAAALEAMKDYTKAMDVYQKALDLDSNCKEAADGYQRCMMAQYNRHDSPEDVKR
          EECIQLEPAFIKGYTRKAAALEAMKDYTKAMDVYQKALDLDS.CKEAADGYQRCMMAQYN.HD.PEDVKR
Retrocopy EECIQLEPAFIKGYTRKAAALEAMKDYTKAMDVYQKALDLDSTCKEAADGYQRCMMAQYNHHDNPEDVKR

Parental  RAMADPEVQQIMSDPAMRLILEQMQKDPQALSEHLKNPVIAQKIQKLMDVGLIAIR
          RAMADPEVQQIMSDPA.RLILEQMQKDPQALSEHLKNPVIAQKIQKL.DVGLIAIR
Retrocopy RAMADPEVQQIMSDPATRLILEQMQKDPQALSEHLKNPVIAQKIQKLTDVGLIAIR

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	6.85 RPM	101.39 RPM
SRP017611_brain	4.92 RPM	99.08 RPM
SRP017611_kidney	4.03 RPM	53.82 RPM
SRP017611_liver	2.03 RPM	29.88 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_474 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_474 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_474 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,