RetrogeneDB ID: retro_btau_836

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 2:116645760..116647389(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000007127
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: STIP1
• Ensembl ID: ENSBTAG00000015663
• Aliases: None
• Description: Stress-induced-phosphoprotein 1 [Source:UniProtKB/Swiss-Prot;Acc:Q3ZBZ8]

Sequence

>retro_btau_836
ATGAAGCAGGTAAATGAGCTCAAAGAGAAGGGCAACAAGGCCCTGAGTGCCGGCAACATTGACGATGCGCTGCAGTGCTA
CTCCGAAGCCATTAAGTTAGACCCCCAGAACCACGTGCTCTACAGCAGTCGCTCCGCGGCCTATGCCAAGAAGGGAGACT
ACCAGAAGGCTTACGAGGACGGCTGCAAGACCGTTGACCTGAAGCCTGACTGGGGCAAGGGCTATTCACGAAAAGCAGCG
GCTCTTGAATTCTTAAACCGATTTGAAGAAGCCAAGCAAACCTATGAGGAGGGTTTAAAACATGAAGCAAACAATCCTCA
GCTCAAAGAAGGTTTACAGAATATGGAGGCCCGGCTGGCAGAAAGGAAATTCATGAACCCTTTCAACATGCCTAATCTGT
ACCAGAAGTTGGAGAGTGATCCCAGGACCAAGACTCTGCTCGCAGATCCTACCTACCGGGAACTGATCGAGCAGCTGCAG
AACAAGCCGTCCGACCTGGGCACGAAACTGCAAGATCCCCGGATCATGACTACTCTTAGCGTCCTGCTCGGAGTTGATCT
GGGCAGTATGGATGAAGAGGAGGAAGTTGCAACACCTCCACCACCACCTCCTCCCAAAAAGGAGACAAAACCAGAGCCAA
TGGAAGAAGATCTTCCAGAGAATAAGAAGCAGGCGCTGAGAGAAAAAGAGCTGGGGAATGAAGCCTACAAGAAGAAAGAC
TTTGACACGGCCTTGAAGCACTACGACAAAGCCAAAGACCTGGATCCCACCAACATGACGTACATAACCAACCAAGCAGC
CGTGTACTTCGAAAAGGGTGACTATGGTCAATGCCGGGAGCTTTGTGAGAAGGCCATTGAAGTGGGGCGAGAAAACCGAG
AAGACTACCGACAGATTGCCAAAGCTTATGCACGAATTGGCAACTCTTACTTCAAAGAAGAAAAGTACAAGGATGCCATC
CATTTCTATAACAAGTCTCTGGCAGAGCACCGAACCCCAGATGTGCTCAAGAAATGCCAGCAGGCAGAGAAAATCTTGAA
GGAGCAAGAGCGGCTGGCCTACATAAACCCTGACCTGGCCTTGGAGGAGAAGAACAAAGGCAATGAGTGTTTTCAGAAAG
GGGACTACCCCCAGGCCATGAAGCACTACACGGAAGCCATCAAACGGAACCCCAAAGACGCCAAGCTGTACAGCAACCGA
GGTGCCTGCTACACCAAGCTCCTGGAGTTCCAGCTGGTGCTCAAGGACTGTGAGGAGTGCATCCAGCTGGAGCCAACCTT
CATCAAGGGTTATACCTGGAAAGCAGCTGCCCTGGAGGCGATGAAGGACTACACGAAAGCCATGGATGTCTACCAGAAAG
CAGTCGACCTGGACTCTAACTGCAAGGAGGCCGCAGATGGTTACCAGCACTGCATGATGGCCCAGTATAACCGACACGAC
AGCCCCGAGGATGTGAAGCGGCGGGCCATGGCCGACCCGGAGGTGCAGCAAATAATGAGTGACCCGGCCATGCGGCTCAT
CCTGGAACAGATGCAGAAGGACCCCCAGGCGCTCAGCGAACACTTAAAGAACCCTGTGATAGCACAGAAGATCCAGAAGC
TGATGGATGTGGGTCTGATAGCCATCCGG

Alignment

ORF - retro_btau_836 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.34 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEQVNELKEKGNKALSAGNIDDALQCYSEAIKLDPQNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLKPD
          M.QVNELKEKGNKALSAGNIDDALQCYSEAIKLDPQNHVLYS.RSAAYAKKGDYQKAYEDGCKTVDLKPD
Retrocopy MKQVNELKEKGNKALSAGNIDDALQCYSEAIKLDPQNHVLYSSRSAAYAKKGDYQKAYEDGCKTVDLKPD

Parental  WGKGYSRKAAALEFLNRFEEAKQTYEEGLKHEANNPQLKEGLQNMEARLAERKFMNPFNMPNLYQKLESD
          WGKGYSRKAAALEFLNRFEEAKQTYEEGLKHEANNPQLKEGLQNMEARLAERKFMNPFNMPNLYQKLESD
Retrocopy WGKGYSRKAAALEFLNRFEEAKQTYEEGLKHEANNPQLKEGLQNMEARLAERKFMNPFNMPNLYQKLESD

Parental  PRTKTLLADPTYRELIEQLRNKPSDLGTKLQDPRIMTTLSVLLGVDLGSMDEEEEVATPPPPPPPKKETK
          PRTKTLLADPTYRELIEQL.NKPSDLGTKLQDPRIMTTLSVLLGVDLGSMDEEEEVATPPPPPPPKKETK
Retrocopy PRTKTLLADPTYRELIEQLQNKPSDLGTKLQDPRIMTTLSVLLGVDLGSMDEEEEVATPPPPPPPKKETK

Parental  PEPMEEDLPENKKQALREKELGNEAYKKKDFDTALKHYDKAKDLDPTNMTYITNQAAVYFEKGDYGQCRE
          PEPMEEDLPENKKQALREKELGNEAYKKKDFDTALKHYDKAKDLDPTNMTYITNQAAVYFEKGDYGQCRE
Retrocopy PEPMEEDLPENKKQALREKELGNEAYKKKDFDTALKHYDKAKDLDPTNMTYITNQAAVYFEKGDYGQCRE

Parental  LCEKAIEVGRENREDYRQIAKAYARIGNSYFKEEKYKDAIHFYNKSLAEHRTPDVLKKCQQAEKILKEQE
          LCEKAIEVGRENREDYRQIAKAYARIGNSYFKEEKYKDAIHFYNKSLAEHRTPDVLKKCQQAEKILKEQE
Retrocopy LCEKAIEVGRENREDYRQIAKAYARIGNSYFKEEKYKDAIHFYNKSLAEHRTPDVLKKCQQAEKILKEQE

Parental  RLAYINPDLALEEKNKGNECFQKGDYPQAMKHYTEAIKRNPKDAKLYSNRAACYTKLLEFQLALKDCEEC
          RLAYINPDLALEEKNKGNECFQKGDYPQAMKHYTEAIKRNPKDAKLYSNR.ACYTKLLEFQL.LKDCEEC
Retrocopy RLAYINPDLALEEKNKGNECFQKGDYPQAMKHYTEAIKRNPKDAKLYSNRGACYTKLLEFQLVLKDCEEC

Parental  IQLEPTFIKGYTRKAAALEAMKDYTKAMDVYQKALDLDSNCKEAADGYQRCVMAQYNRHDSPEDVKRRAM
          IQLEPTFIKGYT.KAAALEAMKDYTKAMDVYQKA.DLDSNCKEAADGYQ.C.MAQYNRHDSPEDVKRRAM
Retrocopy IQLEPTFIKGYTWKAAALEAMKDYTKAMDVYQKAVDLDSNCKEAADGYQHCMMAQYNRHDSPEDVKRRAM

Parental  ADPEVQQIMSDPAMRLILEQMQKDPQALSEHLKNPVIAQKIQKLMDVGLIAIR
          ADPEVQQIMSDPAMRLILEQMQKDPQALSEHLKNPVIAQKIQKLMDVGLIAIR
Retrocopy ADPEVQQIMSDPAMRLILEQMQKDPQALSEHLKNPVIAQKIQKLMDVGLIAIR

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
ERP005899_liver	0.22 RPM	23.50 RPM
ERP005899_muscle	0.32 RPM	101.88 RPM
SRP017611_brain	0.41 RPM	94.05 RPM
SRP017611_kidney	0.47 RPM	73.02 RPM
SRP017611_liver	0.08 RPM	39.87 RPM
SRP030211_testis	0.90 RPM	133.55 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

1 EST(s) were mapped to retro_btau_836 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
DV799254	116646161	116646455	97.2	279	4	264

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_836 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_836 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,