RetrogeneDB ID: retro_btau_611

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 15:84808303..84809334(-)
• Located in intron of: ENSBTAG00000002260

Retrocopy information

• Ensembl ID: ENSBTAG00000046088
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: C8H4orf27
• Ensembl ID: ENSBTAG00000020132
• Aliases: C8H4orf27, C4orf27
• Description: UPF0609 protein C4orf27 homolog [Source:UniProtKB/Swiss-Prot;Acc:A2VDY4]

Sequence

>retro_btau_611
ATGGTGGGCGGTGGCGCGAAGCATAGACTCTGCGGAGAGGGGCCGCAGTGTGAAAAACTGGTCAATGTGAAGAAGAGTAA
GTCCTATGAAGCTGACGTGCCCAGTGACCTTCGAAAAGAGGTGGAAAGCCATTACAGGCTTCTTCTGCCTGAAGATTTCT
ACCACTTCTGGAGGTTCTGCAAAGGACTTGACCCTGAACAGCCAGCTGATTCACTATCTGCAAGCCTTGGACTTCGATTA
GTGGGTCCTTATGATATCCTTGCCGGAAAACATAAAATAAAGAAAAAATCAGCAAGCTTGAATTTTAATCTTCACTGGAG
ATTTTACTATGATCCTCCTGAGTTCCAGACCATTATTATTGGAGACAGTAAAACTCAATTCCACATGGGGTATTTCAGGG
ATTCTCCTGATGAACTTCCTGTATTTGTCGGTACAAACGAAGCAAAGAAAAATTGTATAATTGTTCAAAGTGGAGATAAT
GTGTTTGCTGCAGTCAAATCATTTTTGATGAAAAACTTACAGAAGATAAGAAGAAAACTAGTCTCTTGAAAACCATAGAT
GAGAAACTCACAGAAGCAGCCAGAGAACTGGGGTTCTCCCTGGAGCAGAGAACTGTGAGGGTGAAGCAGAGAGACAAGAA
AGTGGTGACAAAGACCTTTCATGGGGCAGGCTTGGTTGTCCCAGTGGATAAAAATGATGTTGGATACAGAGAGCTCCCTG
AAACGGATGCCAGCCTCAGGAGAATCTGCGGGACAATTGTGGAGGCCCCGAGCAACGCCGACAGACTGCAGGCCTTTGCC
CCCGTCCAGGAGATAATGACCTATGTGCAGCTAGCTAACGATGAGTGCGACTATGGGATGGGGCTGGAGCTGCGGCTGGA
CCTCTTCTGCCATGGCTCCCACTATTTTCATAAAGTTGCTGGCCAGCTTTTACCTCTGGCATATAATCTGCTGAAGAGGA
ATCTCTTTGCGGAAATTAATGAAGCTCATCTAGCAAACAGGAGCCAAGAGGACGTGGACCAGCTCGCAGCA

Alignment

ORF - retro_btau_611 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.66 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MVGGGAKRRLRGEGPQCEKPVDMKKSKSCEADVPGDLRKEVESHYRLPLPEDFYHFWRFCEGLDPEQPAD
          MVGGGAK.RL.GEGPQCEK.V..KKSKS.EADVP.DLRKEVESHYRL.LPEDFYHFWRFC.GLDPEQPAD
Retrocopy MVGGGAKHRLCGEGPQCEKLVNVKKSKSYEADVPSDLRKEVESHYRLLLPEDFYHFWRFCKGLDPEQPAD

Parental  SLSASLGLRLVGPYDILAGKHKIKKKSASLNFNLHWRFYYDPPEFQTIIIGDSKTQFHMGYFRDSPDELP
          SLSASLGLRLVGPYDILAGKHKIKKKSASLNFNLHWRFYYDPPEFQTIIIGDSKTQFHMGYFRDSPDELP
Retrocopy SLSASLGLRLVGPYDILAGKHKIKKKSASLNFNLHWRFYYDPPEFQTIIIGDSKTQFHMGYFRDSPDELP

Parental  VFVGTNEAKKNCIIVQSGDNVFAAVKLFLMK-KLKEVTDKKKSSLLKTIDEKLTEAARELGFSLEQRTVR
          VFVGTNEAKKNCIIVQSGDNVFAAVK.FLMK.KL.E..DKKK.SLLKTIDEKLTEAARELGFSLEQRTVR
Retrocopy VFVGTNEAKKNCIIVQSGDNVFAAVKSFLMK<KLTE--DKKKTSLLKTIDEKLTEAARELGFSLEQRTVR

Parental  MKQRDKKVVTKTFHGAGLVVPVDKNDVGYRELPETDASLRRICGTIVEAPSDADRLQAFAPVQEMMTYVQ
          .KQRDKKVVTKTFHGAGLVVPVDKNDVGYRELPETDASLRRICGTIVEAPS.ADRLQAFAPVQE.MTYVQ
Retrocopy VKQRDKKVVTKTFHGAGLVVPVDKNDVGYRELPETDASLRRICGTIVEAPSNADRLQAFAPVQEIMTYVQ

Parental  FANDECDYGMGLELGLDLFCHGSHYFHKVAGQLLPLAYNLLKRNLFAEIIEAHLANRSQDDVDQLAA
          .ANDECDYGMGLEL.LDLFCHGSHYFHKVAGQLLPLAYNLLKRNLFAEI.EAHLANRSQ.DVDQLAA
Retrocopy LANDECDYGMGLELRLDLFCHGSHYFHKVAGQLLPLAYNLLKRNLFAEINEAHLANRSQEDVDQLAA

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	10.02 RPM
ERP005899_muscle	0.53 RPM	9.77 RPM
SRP017611_brain	0.14 RPM	8.41 RPM
SRP017611_kidney	0.12 RPM	10.37 RPM
SRP017611_liver	0.00 RPM	3.62 RPM
SRP030211_testis	0.73 RPM	39.78 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_611 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_611 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_611 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020132	1 retrocopy	retro_btau_611 ,
Equus caballus	ENSECAG00000013735	1 retrocopy	retro_ecab_551,
Gorilla gorilla	ENSGGOG00000003090	1 retrocopy	retro_ggor_2306,
Myotis lucifugus	ENSMLUG00000017052	1 retrocopy	retro_mluc_395,
Ictidomys tridecemlineatus	ENSSTOG00000001481	1 retrocopy	retro_itri_101,
Tursiops truncatus	ENSTTRG00000009751	1 retrocopy	retro_ttru_862,