RetrogeneDB ID: retro_btau_1600

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 8:21903594..21904914(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BT.62921
• Ensembl ID: ENSBTAG00000011843
• Aliases: None
• Description: elongation factor 1-gamma [Source:RefSeq peptide;Acc:NP_001035577]

Sequence

>retro_btau_1600
ATGGCGGCTGGGACCCTGTACACATATCCTGAAAACTGGAGGGCCTTCAAGGCCCTCATTGCCGCTCAGTACAGCGGGGC
TCAGGTCCGCGTGCTCTCCGCACCACCCCACTTCCATTTTGGCCAAACCAACCGCACCCCCGAATTTCTCCGCAAATTTC
CTGCTGGCAAGGTTCCAGCCTTTGAGGGTGACGATGGATTCTGTGTGTTCGACAGCAATGCCATTGCCTACTATGTGAGC
AACGAGGAGCTGCGGGGAAGTACTCCCGAGGCAGCAGCGCAGGTGGTGCAGTGGGTGAGCTTTGCTGATAGCGACATAGT
GCCACCGGCCAGCACCTGGGTGTTCCCTACCTTGGGCATCATGCACCACAACAAGCAGGCCACAGAGAATGCAAAGGAGG
AGATGAGGCGAATTCTGGGGCTGCTGGATGCTCACTTGAAGACGAGAACTTTTCTGGTGGGCGAACGCGTGACGCTGGCT
GACATCACAGTTGTCTGCACCCTGCTGTAGCTTTACAAACAGGTTCTGGAGCCTTCTTTTCGCCAGGCCTTCCCTAATAC
CAACCACTGGTTCCTCACCTGCATTAACCAGCCCCAGTTCCGGGCTGTCTTGGGAGAGGTGAAACTCTGTGAGAAAATGG
CCCAGTTTGATGCTAAAAAGTTTGCAGAGAGCCAGCCTAAAAAGGACACCCCACGGAAGGAGAAAGGTTCTCGAGAAGAG
AAGCCGAAGCCCCAGGTGGAGCGGAAGGAGGGCAAAGAGGAGAAGAAGGCGGCTGCCCCCTCTCCTGAGGAGGAGCTGGA
TGAATGTGAGCAGGCGCTGGCTGCCGAGCCGAAGGCCAAGGATCCTTTTGCCCATCTGCCCAAGAGTACCTTTGTGTTGG
ATGAATTTAAGCGCAAGTACTCCAACGAGGATACGCTCTCCGTGGCGCTGCCGTACTTTTGGGATCACTTTGATAAGGAT
GGCTGGTCCCTGTGGTACTCTGAGTATCGCTTCCCTGAAGAGCTCACCCAGACCTTCATGAGTTGCAACCTCATCACTGG
AATGTTCCAGCGATTGGACAAACTGAGGAAGAATGCCTTTGCCAGTGTCATTCTCTTTGGAACCAACAATAGCAGCTCCA
TTTCTGGGGTCTGGGTCTTTCGAGGCCAGGAGCTTGCTTTTCTGCTGAGTCCAGATTGGCAGGTGGACTAGGAGTCATAC
ACATGGCGGAAACTGGATCCCGGCAGCGAGGAGACCCAGACGCTGGTTCGAGAATACTTTTGCTGGGAAGGGGCCTTCCA
GCATGTGGGCAAAGCCTTCAATCAGGGCAAGATCTTCAAA

Alignment

ORF - retro_btau_1600 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.95 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAGTLYTYPENWRAFKALIAAQYSGAQVRVLSAPPHFHFGQTNRTPEFLRKFPAGKVPAFEGDDGFCVF
          MAAGTLYTYPENWRAFKALIAAQYSGAQVRVLSAPPHFHFGQTNRTPEFLRKFPAGKVPAFEGDDGFCVF
Retrocopy MAAGTLYTYPENWRAFKALIAAQYSGAQVRVLSAPPHFHFGQTNRTPEFLRKFPAGKVPAFEGDDGFCVF

Parental  ESNAIAYYVSNEELRGSTPEAAAQVVQWVSFADSDIVPPASTWVFPTLGIMHHNKQATENAKEEVRRILG
          .SNAIAYYVSNEELRGSTPEAAAQVVQWVSFADSDIVPPASTWVFPTLGIMHHNKQATENAKEE.RRILG
Retrocopy DSNAIAYYVSNEELRGSTPEAAAQVVQWVSFADSDIVPPASTWVFPTLGIMHHNKQATENAKEEMRRILG

Parental  LLDAHLKTRTFLVGERVTLADITVVCTLLWLYKQVLEPSFRQAFPNTNRWFLTCINQPQFRAVLGEVKLC
          LLDAHLKTRTFLVGERVTLADITVVCTLL.LYKQVLEPSFRQAFPNTN.WFLTCINQPQFRAVLGEVKLC
Retrocopy LLDAHLKTRTFLVGERVTLADITVVCTLL*LYKQVLEPSFRQAFPNTNHWFLTCINQPQFRAVLGEVKLC

Parental  EKMAQFDAKKFAESQPKKDTPRKEKGSREEKLKPQAERKEGKEEKKAAAPAPEEELDECEQALAAEPKAK
          EKMAQFDAKKFAESQPKKDTPRKEKGSREEK.KPQ.ERKEGKEEKKAAAP.PEEELDECEQALAAEPKAK
Retrocopy EKMAQFDAKKFAESQPKKDTPRKEKGSREEKPKPQVERKEGKEEKKAAAPSPEEELDECEQALAAEPKAK

Parental  DPFAHLPKSTFVLDEFKRKYSNEDTLSVALPYFWDHFDKDGWSLWYSEYRFPEELTQTFMSCNLITGMFQ
          DPFAHLPKSTFVLDEFKRKYSNEDTLSVALPYFWDHFDKDGWSLWYSEYRFPEELTQTFMSCNLITGMFQ
Retrocopy DPFAHLPKSTFVLDEFKRKYSNEDTLSVALPYFWDHFDKDGWSLWYSEYRFPEELTQTFMSCNLITGMFQ

Parental  RLDKLRKNAFASVILFGTNNSSSISGVWVFRGQELAFPLSPDWQVDYESYTWRKLDPGSEETQTLVREYF
          RLDKLRKNAFASVILFGTNNSSSISGVWVFRGQELAF.LSPDWQVD.ESYTWRKLDPGSEETQTLVREYF
Retrocopy RLDKLRKNAFASVILFGTNNSSSISGVWVFRGQELAFLLSPDWQVD*ESYTWRKLDPGSEETQTLVREYF

Parental  CWEGAFQHVGKAFNQGKIFK
          CWEGAFQHVGKAFNQGKIFK
Retrocopy CWEGAFQHVGKAFNQGKIFK

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	0.50 RPM	126.46 RPM
ERP005899_muscle	4.80 RPM	1173.92 RPM
SRP017611_brain	0.96 RPM	130.41 RPM
SRP017611_kidney	1.30 RPM	333.46 RPM
SRP017611_liver	2.19 RPM	212.48 RPM
SRP030211_testis	5.91 RPM	573.82 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1600 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1600 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1600 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 36 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000011843	1 retrocopy	retro_btau_1600 ,
Canis familiaris	ENSCAFG00000015834	6 retrocopies	retro_cfam_1241, retro_cfam_1398, retro_cfam_1862, retro_cfam_478, retro_cfam_638, retro_cfam_653,
Callithrix jacchus	ENSCJAG00000018949	6 retrocopies	retro_cjac_1464, retro_cjac_1770, retro_cjac_1942, retro_cjac_3147, retro_cjac_841, retro_cjac_874,
Latimeria chalumnae	ENSLACG00000014700	1 retrocopy	retro_lcha_82,
Myotis lucifugus	ENSMLUG00000000342	1 retrocopy	retro_mluc_1110,
Monodelphis domestica	ENSMODG00000007691	1 retrocopy	retro_mdom_68,
Nomascus leucogenys	ENSNLEG00000003528	2 retrocopies	retro_nleu_1510, retro_nleu_681,
Otolemur garnettii	ENSOGAG00000000827	1 retrocopy	retro_ogar_1344,
Ochotona princeps	ENSOPRG00000014563	1 retrocopy	retro_opri_814,
Pan troglodytes	ENSPTRG00000003768	3 retrocopies	retro_ptro_1879, retro_ptro_2017, retro_ptro_3159,
Pteropus vampyrus	ENSPVAG00000003440	1 retrocopy	retro_pvam_1239,
Rattus norvegicus	ENSRNOG00000020075	8 retrocopies	retro_rnor_1312, retro_rnor_2126, retro_rnor_2235, retro_rnor_2269, retro_rnor_2468, retro_rnor_2617, retro_rnor_2928, retro_rnor_979,
Sus scrofa	ENSSSCG00000013064	1 retrocopy	retro_sscr_164,
Tursiops truncatus	ENSTTRG00000002459	3 retrocopies	retro_ttru_1082, retro_ttru_1544, retro_ttru_1603,