RetrogeneDB ID: retro_btau_1338

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 4:9014816..9015481(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NFYC
• Ensembl ID: ENSBTAG00000021943
• Aliases: None
• Description: Nuclear transcription factor Y subunit gamma [Source:UniProtKB/Swiss-Prot;Acc:Q5E9X1]

Sequence

>retro_btau_1338
ATGTCCCCAGGAGGGGGATTTGGTGGTGCTAGCAGCAGTGGTGCCCAGCAAACTCTGCATTCCTTCTGGCCTCGTGTCAC
GGGAGAAATCTGGAATTTAACAGTGAAAGATTTCTGAGTACAGAAACTCCCACTGGCTCGTATTAAGAAGATTATGAAAC
TGGCTGGCGATGTGAAGATGGTCAGTGCAGAAGCCCCTGTGTTGTTTGCCAAGGAAGCCCAGATTTTTATCACAGAGTTG
ACTCTTGGGGCCTGGATCCACACAGAGGAGAACCAGCACCAGACTCTTCAGAGGCATGACATTGCCATGGCAATTACAAG
ATGTGATGAGTTTGACTTTCTCACTGATGTTCCGAGAGATGAGTGGAAACCAGCAAAGCATCAGGAGAAGCTGCGCTGGT
ATGTGACTCTTGCTGAACCTGTCCAGGACTGCTGCAGGTTGGCTCAGCAGCCCACTGCCGATCAAGTCCCGGGGCAGCAG
CAAGGCCAGCAGACCCCCAGCTCCACAAGCACCATCAAGCCTGGGCAGATCATTGTTGCACAGCCTCAGAAGGGCCAGAC
CACACCCGTGACCATGCAGGTGAAGAAGGTCAGCAGGTCCAGGCCCATCCACACGGTCAAGCCCAGCAGGCCCAGAGCGG
CACTGAATGGACCGTGCAGGTGATG

Alignment

ORF - retro_btau_1338 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.77 %
• Parental protein coverage: 67.66 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSTEGGFGGAGSSDAQQSLQSFWPRVMEEIRNLTVKDFRVQELPLARIKKIMKLDEDVKMISAEAPVLFA
          MS..GGFGGA.SS.AQQ.L.SFWPRV..EI.NLTVKDF.VQ.LPLARIKKIMKL..DVKM.SAEAPVLFA
Retrocopy MSPGGGFGGASSSGAQQTLHSFWPRVTGEIWNLTVKDF*VQKLPLARIKKIMKLAGDVKMVSAEAPVLFA

Parental  KAAQIFITELTLRAWIHTEDNKRRTLQRNDIAMAITKFDQFDFLIDIVPRDELKPPKRQEEVRQSVTPAE
          K.AQIFITELTL.AWIHTE.N...TLQR.DIAMAIT..D.FDFL.D.VPRDE.KP.K.QE..R..VT.AE
Retrocopy KEAQIFITELTLGAWIHTEENQHQTLQRHDIAMAITRCDEFDFLTD-VPRDEWKPAKHQEKLRWYVTLAE

Parental  PVQYYFTLAQQPTAVQVQGQQQGQQTTSSTTTIQPGQIIIAQPQQGQTTPVTMQV-GEGQQVQIVQAQPQ
          PVQ....LAQQPTA.QV.GQQQGQQT.SST.TI.PGQII.AQPQ.GQTTPVTMQV..EGQQVQ...A.P.
Retrocopy PVQDCCRLAQQPTADQVPGQQQGQQTPSSTSTIKPGQIIVAQPQKGQTTPVTMQV<EEGQQVQ---AHPH

Parental  GQAQQAQSGTGQTMQVM
          GQAQQAQSGT..T.QVM
Retrocopy GQAQQAQSGTEWTVQVM

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	0.00 RPM	11.75 RPM
ERP005899_muscle	0.00 RPM	22.75 RPM
SRP017611_brain	0.00 RPM	17.81 RPM
SRP017611_kidney	0.00 RPM	50.68 RPM
SRP017611_liver	0.00 RPM	16.31 RPM
SRP030211_testis	0.05 RPM	36.95 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1338 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1338 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1338 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000012591	1 retrocopy	retro_acar_33,
Bos taurus	ENSBTAG00000021943	1 retrocopy	retro_btau_1338 ,
Callithrix jacchus	ENSCJAG00000002987	1 retrocopy	retro_cjac_4050,
Homo sapiens	ENSG00000066136	2 retrocopies	retro_hsap_4280, retro_hsap_4668,
Gorilla gorilla	ENSGGOG00000007360	2 retrocopies	retro_ggor_2865, retro_ggor_2896,
Macropus eugenii	ENSMEUG00000004480	1 retrocopy	retro_meug_1145,
Macaca mulatta	ENSMMUG00000014970	2 retrocopies	retro_mmul_1202, retro_mmul_2485,
Mus musculus	ENSMUSG00000032897	1 retrocopy	retro_mmus_844,
Otolemur garnettii	ENSOGAG00000012614	2 retrocopies	retro_ogar_2147, retro_ogar_411,
Pongo abelii	ENSPPYG00000001483	3 retrocopies	retro_pabe_1712, retro_pabe_3490, retro_pabe_3628,
Pan troglodytes	ENSPTRG00000000596	2 retrocopies	retro_ptro_2903, retro_ptro_3102,