RetrogeneDB ID: retro_btau_870

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 2:50561642..50562356(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BT.65854
• Ensembl ID: ENSBTAG00000012873
• Aliases: None
• Description: sorting nexin-6 [Source:RefSeq peptide;Acc:NP_001039796]

Sequence

>retro_btau_870
CTTAAAGCAATAAATGTAGATTTTCAGAGTGATGCTGCTCTGCACGTGGACATTTCTGATGCTCTGAGTGAGAGAGACAA
AGTAAAATTCACTGTTCACACAAAGAGTTCATTGCTAAATTTTAAACAGAATGAGTTTTCTGTTGTTCGACAACATGAGG
AATTTATCTGGCTTCACGATTCCTTCATTGAAAATGAAGACTATGCAGGTTACATTATTCCTCCAGCACCACCAAGACCT
GATTTTGATGCCTCAAGGGAGAAACTACAGAAACTTGGAGAAGGAGAAGGGTCTATGACGAAGGAGGAATTCACGAAGAT
GAAACAGGAATTGGAAGCTGAGTATTTGGCAATATTCAAGAAGACGGTTGCAATGCATGAAGTGTTTCTGTGTCGTGTGG
CTGCACATCCCATTTTGAGGAAAGATTTAAATTTCCATGTCTTCCTGGAATATAATCAAGATTTGAGTGTGCGAGGAAAA
AATAAAAAAGAGAAACTAGAAGATTTCCTTAAAAACATGGTTAAATCAGCAGATGGAGTAATTGTTTCTGGAGTAAAGGA
TGTAGATGATTTCTTTGAGCATGAATGAACATTCCTTTTAGAATATTATAACCGAGTTAAGGATGCATCTGCTAAATCTG
ATAAGATGACAAGATCCCACAAAAGTGCTGCAGATGATTACAATAGAATTGGTTCTTCATTTTATGATTTAGGA

Alignment

ORF - retro_btau_870 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.12 %
• Parental protein coverage: 61.34 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LKAINVDLQSDAALQVDISDALSERDKVKFTVHTKSSLPNFKQNEFSVVRQHEEFIWLHDSFIENEDYAG
          LKAINVD.QSDAAL.VDISDALSERDKVKFTVHTKSSL.NFKQNEFSVVRQHEEFIWLHDSFIENEDYAG
Retrocopy LKAINVDFQSDAALHVDISDALSERDKVKFTVHTKSSLLNFKQNEFSVVRQHEEFIWLHDSFIENEDYAG

Parental  YIIPPAPPRPDFDASREKLQKLGEGEGSMTKEEFTKMKQELEAEYLAIFKKTVAMHEVFLCRVAAHPILR
          YIIPPAPPRPDFDASREKLQKLGEGEGSMTKEEFTKMKQELEAEYLAIFKKTVAMHEVFLCRVAAHPILR
Retrocopy YIIPPAPPRPDFDASREKLQKLGEGEGSMTKEEFTKMKQELEAEYLAIFKKTVAMHEVFLCRVAAHPILR

Parental  KDLNFHVFLEYNQDLSVRGKNKKEKLEDFFKNMVKSADGVIVSGVKDVDDFFEHERTFLLEYHNRVKDAS
          KDLNFHVFLEYNQDLSVR.....EKLEDF.KNMVKSADGVIVSGVKDVDDFFEHE.TFLLEY.NRVKDAS
Retrocopy KDLNFHVFLEYNQDLSVRXXXXXEKLEDFLKNMVKSADGVIVSGVKDVDDFFEHE*TFLLEYYNRVKDAS

Parental  AKSDRMTRSHKSAADDYNRIGSSLYALG
          AKSD.MTRSHKSAADDYNRIGSS.Y.LG
Retrocopy AKSDKMTRSHKSAADDYNRIGSSFYDLG

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	23.29 RPM
ERP005899_muscle	1.37 RPM	49.04 RPM
SRP017611_brain	1.05 RPM	18.00 RPM
SRP017611_kidney	2.13 RPM	34.73 RPM
SRP017611_liver	0.91 RPM	9.89 RPM
SRP030211_testis	2.24 RPM	56.92 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_870 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_870 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_870 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012873	1 retrocopy	retro_btau_870 ,
Cavia porcellus	ENSCPOG00000006862	1 retrocopy	retro_cpor_1145,
Nomascus leucogenys	ENSNLEG00000003310	1 retrocopy	retro_nleu_3063,
Pongo abelii	ENSPPYG00000005736	2 retrocopies	retro_pabe_1668, retro_pabe_1698,
Pan troglodytes	ENSPTRG00000006253	1 retrocopy	retro_ptro_1362,