RetrogeneDB ID: retro_btau_527

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 13:48173112..48174045(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF3F
• Ensembl ID: ENSBTAG00000004861
• Aliases: None
• Description: None

Sequence

>retro_btau_527
CCCGCGTCATCCTCAGACCTGGCAGCAGCAGCGGCTACGACCGCGGCTCCGGGCCAGACCCCGGCCTCAGCGCCAGCCCC
AGCGCAGACCCCCGCACAGTCTCTGTCCGGCCCTGCTCTCCCAGGCCCCTTCCCCGGCGGCCGCGTGGTCCGGCTGCACC
CGGTCATTTTGGCCTCCATCGTGAACAGCTACGAGCGACGCAACGAGGGAGCTGCCTGAGTTATCGCGGCCCTGCTGGGA
AGCGTTGACAAGCACTCAGTGGAAGTCACCAATTGCTTTTCAGTGCCACACAAAGAGTCAGAAGATGAGGTGGCTGTTGA
CATGGAGTTTGCTAAGAACATGTATGAGTTGCACAAGAAAGTCTCTCCAAATGAGCTCATCCTGGGCTGGTACGCTACAG
GCCATGACATGACAGAGCACTCAGTGCTGATCCATGAGTACTACAGCCGAGAAGCCCCCAACCCCATTCACCTCACAGTG
GACACCAGCCTCCAGAACGGCCGCATGAGCATCAGCACTTTAATGGGTGTTCCTGGGAGGACCATGGGGGTGATGTTCAC
CCCTCTGACAGTGAAATACACGCATTACGACACTGAACTCATTGGAGTTGACCTGATCATGAGGACCTGTTTTAGCCCCA
ACCGGGTGATCGGCCTCTCCAGTGACTTGCAGCAAGTGGGCGGGGCTTCTGCTCGCTTCCAGGACGCCCTCAGCACAGTG
TTGCAGTATGCGGAGGATGTGCTGTCTGGAAAGGTGTCAGCCGACAATACCGTGGGTCGCTTCTTGATGAGTCTGGTTAA
CCAAGTACCCAAAATAGTTCCCGAGGACATCGAGACCATGCTCAACAGCAACATCAACGACCTGTTGATGGTAACCTATC
TGGCCAACCTCACACAGTCACAAATTGCCCTCGATAAGAAGCTTGTGAACCTG

Alignment

ORF - retro_btau_527 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.97 %
• Parental protein coverage: 82.03 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PASSSDPAAAAATTAAPGQTPASAPAPAQTPAQSLSGPALPGPFPGGRVVRLHPVILASIVDSYERRNEG
          PASSSD.AAAAATTAAPGQTPASAPAPAQTPAQSLSGPALPGPFPGGRVVRLHPVILASIV.SYERRNEG
Retrocopy PASSSDLAAAAATTAAPGQTPASAPAPAQTPAQSLSGPALPGPFPGGRVVRLHPVILASIVNSYERRNEG

Parental  AARVIGTLLGTVDKHSVEVTNCFSVPHNESEDEVAVDMEFAKNMYELHKKVSPNELILGWYATGHDITEH
          AA.VI..LLG.VDKHSVEVTNCFSVPH.ESEDEVAVDMEFAKNMYELHKKVSPNELILGWYATGHD.TEH
Retrocopy AA*VIAALLGSVDKHSVEVTNCFSVPHKESEDEVAVDMEFAKNMYELHKKVSPNELILGWYATGHDMTEH

Parental  SVLIHEYYSREAPNPIHLTVDTSLQNGRMSIKAYVSTLMGVPGRTMGVMFTPLTVKYTYYDTERIGVDLI
          SVLIHEYYSREAPNPIHLTVDTSLQNGRMSI....STLMGVPGRTMGVMFTPLTVKYT.YDTE.IGVDLI
Retrocopy SVLIHEYYSREAPNPIHLTVDTSLQNGRMSI----STLMGVPGRTMGVMFTPLTVKYTHYDTELIGVDLI

Parental  MKTCFSPNRVIGLSSDLQQVGGASARIQDALSTVLQYAEDVLSGKVSADNTVGRFLMSLVNQVPKIVPED
          M.TCFSPNRVIGLSSDLQQVGGASAR.QDALSTVLQYAEDVLSGKVSADNTVGRFLMSLVNQVPKIVPED
Retrocopy MRTCFSPNRVIGLSSDLQQVGGASARFQDALSTVLQYAEDVLSGKVSADNTVGRFLMSLVNQVPKIVPED

Parental  FETMLNSNINDLLMVTYLANLTQSQIALNEKLVNL
          .ETMLNSNINDLLMVTYLANLTQSQIAL..KLVNL
Retrocopy IETMLNSNINDLLMVTYLANLTQSQIALDKKLVNL

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	23.14 RPM
ERP005899_muscle	0.37 RPM	209.20 RPM
SRP017611_brain	0.00 RPM	61.94 RPM
SRP017611_kidney	0.06 RPM	72.67 RPM
SRP017611_liver	0.00 RPM	53.91 RPM
SRP030211_testis	0.27 RPM	34.77 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_527 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_527 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_527 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004861	1 retrocopy	retro_btau_527 ,
Canis familiaris	ENSCAFG00000006884	1 retrocopy	retro_cfam_1339,
Callithrix jacchus	ENSCJAG00000011903	1 retrocopy	retro_cjac_1416,
Erinaceus europaeus	ENSEEUG00000001226	1 retrocopy	retro_eeur_130,
Echinops telfairi	ENSETEG00000002717	2 retrocopies	retro_etel_1583, retro_etel_35,
Homo sapiens	ENSG00000175390	3 retrocopies	retro_hsap_2106, retro_hsap_2512, retro_hsap_4321,
Gorilla gorilla	ENSGGOG00000011702	5 retrocopies	retro_ggor_1566, retro_ggor_1567, retro_ggor_1568, retro_ggor_1589, retro_ggor_1590,
Myotis lucifugus	ENSMLUG00000000825	1 retrocopy	retro_mluc_2356,
Macaca mulatta	ENSMMUG00000015010	1 retrocopy	retro_mmul_412,
Oryctolagus cuniculus	ENSOCUG00000004225	1 retrocopy	retro_ocun_1488,
Otolemur garnettii	ENSOGAG00000003220	3 retrocopies	retro_ogar_3041, retro_ogar_859, retro_ogar_863,
Pongo abelii	ENSPPYG00000003512	1 retrocopy	retro_pabe_175,
Pan troglodytes	ENSPTRG00000003326	1 retrocopy	retro_ptro_197,
Pteropus vampyrus	ENSPVAG00000015764	1 retrocopy	retro_pvam_371,