RetrogeneDB ID: retro_btau_762

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 19:41827201..41827910(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMBIM6
• Ensembl ID: ENSBTAG00000018588
• Aliases: TMBIM6, TEGT
• Description: Bax inhibitor 1 [Source:UniProtKB/Swiss-Prot;Acc:Q0V882]

Sequence

>retro_btau_762
ATGCATAAATTTGATCGGAAGATCAACTTTGATGCACTCTTTAAATTTTCCCACATAACCCCCTCGACACAGCAGCACCT
GAAGAAGGTCTCTGCCAGTTTTGTCTTCTGTATGTTTGTGGTGGCTGCAGGGGCCTATGTCCATGTGGTCACCCATTTCA
TTCAGGCTGGCCTGCTCTCTGCCTTGGGCTCTCTGGGGTTGATGATTCGGCTGATGGCAACACCTCACAGCCATGAATAT
AAGCAAAAAAAGACTGGGACTTCTGGCTGGATTTGCTTTCCTTACAGGAGTTGGCCTGGGCCTTGCTCTGGACTTGTGCA
CTGCCATCAACCCCAGCATCCTTCTCACTGCCTTCATGGTCCCAGCAATGATCTTCACTTGCTTCACCCTGAGTGCACTC
TGTGCCAGGTGCCATAACTACTTCTTTCTAGGAGGTATCTTGATGTCAGCCATGAGCCTGATGCTCTTGTCTTTCCTGGG
GAACCTATTCTTCGGATCTATTTGGCTTTTCCAGGCAAGCCTGTATGTGGGGCTGGTGGTCATGTGTGGCTTTGTCCTTT
TTGATACTCAACTCATTATTGAAAAGGCTGAAAATGGAGATAAAGATTATATCTGGCATTGTGTTGACCTCTTCTTAGAT
TTTGTAACTCTCTTCAGAAAGTTCATGATGATCCTGGCTATGAATGGGAAGAATAATAAGAAGAAGCGA

Alignment

ORF - retro_btau_762 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.34 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MNIFDRKINFDALFKFSHITPSTQQHLKKVYASFALCMFVAAAGAYIHVVTHFIQAGLLSALGSLGLMIW
          M..FDRKINFDALFKFSHITPSTQQHLKKV.ASF..CMFV.AAGAY.HVVTHFIQAGLLSALGSLGLMI.
Retrocopy MHKFDRKINFDALFKFSHITPSTQQHLKKVSASFVFCMFVVAAGAYVHVVTHFIQAGLLSALGSLGLMIR

Parental  LMATPHSHETEQK-RLGLLAGFAFLTGVGLGPALDLCIAINPSILPTAFMGTAMIFTCFTLSALYARRRS
          LMATPHSHE..QK.RLGLLAGFAFLTGVGLG.ALDLC.AINPSIL.TAFM..AMIFTCFTLSAL.AR...
Retrocopy LMATPHSHEYKQK>RLGLLAGFAFLTGVGLGLALDLCTAINPSILLTAFMVPAMIFTCFTLSALCARCHN

Parental  YLFLGGILMSAMSLMLLSSLGNLFFGSVWLFQANLYMGLVVMCGFVLFDTQLIIEKAENGDKDYIWHCVD
          Y.FLGGILMSAMSLMLLS.LGNLFFGS.WLFQA.LY.GLVVMCGFVLFDTQLIIEKAENGDKDYIWHCVD
Retrocopy YFFLGGILMSAMSLMLLSFLGNLFFGSIWLFQASLYVGLVVMCGFVLFDTQLIIEKAENGDKDYIWHCVD

Parental  LFLDFVTLFRKLMMILAMNEKDKKKKK
          LFLDFVTLFRK.MMILAMN.K..KKK.
Retrocopy LFLDFVTLFRKFMMILAMNGKNNKKKR

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	0.07 RPM	1883.22 RPM
ERP005899_muscle	0.26 RPM	1096.96 RPM
SRP017611_brain	0.00 RPM	402.94 RPM
SRP017611_kidney	0.12 RPM	1202.92 RPM
SRP017611_liver	0.08 RPM	1065.88 RPM
SRP030211_testis	0.07 RPM	170.08 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_762 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_762 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_762 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000018588	1 retrocopy	retro_btau_762 ,
Canis familiaris	ENSCAFG00000008400	2 retrocopies	retro_cfam_1220, retro_cfam_876,
Callithrix jacchus	ENSCJAG00000021032	1 retrocopy	retro_cjac_272,
Dasypus novemcinctus	ENSDNOG00000007882	2 retrocopies	retro_dnov_164, retro_dnov_857,
Macropus eugenii	ENSMEUG00000015590	4 retrocopies	retro_meug_1076, retro_meug_1706, retro_meug_2157, retro_meug_48,
Monodelphis domestica	ENSMODG00000004277	2 retrocopies	retro_mdom_210, retro_mdom_250,
Otolemur garnettii	ENSOGAG00000005137	2 retrocopies	retro_ogar_1074, retro_ogar_3470,
Pteropus vampyrus	ENSPVAG00000016821	1 retrocopy	retro_pvam_755,
Sarcophilus harrisii	ENSSHAG00000010366	1 retrocopy	retro_shar_622,
Ictidomys tridecemlineatus	ENSSTOG00000001165	2 retrocopies	retro_itri_1273, retro_itri_564,
Tarsius syrichta	ENSTSYG00000002427	1 retrocopy	retro_tsyr_916,