RetrogeneDB ID: retro_btau_1390

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 5:77560213..77560755(+)
• Located in intron of: ENSBTAG00000011395

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARF1
• Ensembl ID: ENSBTAG00000007725
• Aliases: None
• Description: ADP-ribosylation factor 1 [Source:UniProtKB/Swiss-Prot;Acc:P84080]

Sequence

>retro_btau_1390
ATGGGGAATATCTTTGCAAACCTATTTAAGGGCCTTTTTGGCAAAAAAGAAATGTGCGTTCTCATGGTGGGCCTAGATGC
TGCCGGAAAGACCACCATCCTGTACAAACTAAAGCTAGGTTAAATGGTGACCACCATTCCCACTAATAGGCTTCAATGTG
GAGACCGTGGAATACAAGAACATCAGCTTCACTGCGTCGGACATGGGGGGCCAGGACAAGACCTGGCCTCTGTGGTACCA
CTACTTCCAAATCACACAACGTCTCATCTTTGTGGTCGACAGCAGTGACACAGAGCATGTGAATGAGGTCCACAAGGAGC
TCATGAGGATGCTAGCAGAAGACAAGCTCAGGGACACTGTTCTGCTCATGTTTGCTAACAAATAGGACCTTCCCAATGCC
ATGATGCAGCCAAGATCACAGACACGCTAGGTCTGCACACTCTGCGCCACAGGAATTGGTACATTCAGGCCACCTGTGTC
TCCAGTGGGGATGGGTCTATGAGGGACTGGACTGGCTGTCCAATCAGCTCCAGAACCAGAAA

Alignment

ORF - retro_btau_1390 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.07 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MGNIFANLFKGLFGKKEMRILMVGLDAAGKTTILYKLKLGEIVTTIPT-IGFNVETVEYKNISFTVWDVG
          MGNIFANLFKGLFGKKEM..LMVGLDAAGKTTILYKLKLG..VTTIPT.IGFNVETVEYKNISFT..D.G
Retrocopy MGNIFANLFKGLFGKKEMCVLMVGLDAAGKTTILYKLKLG*MVTTIPT>IGFNVETVEYKNISFTASDMG

Parental  GQDKIRPLWRHYFQNTQGLIFVVDSNDRERVNEAREELMRMLAEDELRDAVLLVFANKQDLPNAM-NAAE
          GQDK..PLW.HYFQ.TQ.LIFVVDS.D.E.VNE...ELMRMLAED.LRD.VLL.FANK.DLPNAM..AA.
Retrocopy GQDKTWPLWYHYFQITQRLIFVVDSSDTEHVNEVHKELMRMLAEDKLRDTVLLMFANK*DLPNAM<DAAK

Parental  ITDKLGLHSLRHRNWYIQATCATSGDG-LYEGLDWLSNQLRNQK
          ITD.LGLH.LRHRNWYIQATC..SGDG..YEGLDWLSNQL.NQK
Retrocopy ITDTLGLHTLRHRNWYIQATCVSSGDG<VYEGLDWLSNQLQNQK

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	30.50 RPM
ERP005899_muscle	0.16 RPM	186.87 RPM
SRP017611_brain	0.05 RPM	78.98 RPM
SRP017611_kidney	0.12 RPM	138.64 RPM
SRP017611_liver	0.00 RPM	90.31 RPM
SRP030211_testis	0.06 RPM	134.72 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1390 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1390 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1390 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 51 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006785	1 retrocopy	retro_btau_26,
Bos taurus	ENSBTAG00000007725	2 retrocopies	retro_btau_1257, retro_btau_1390 ,
Bos taurus	ENSBTAG00000016069	1 retrocopy	retro_btau_542,
Callithrix jacchus	ENSCJAG00000016671	10 retrocopies	retro_cjac_1295, retro_cjac_1691, retro_cjac_1719, retro_cjac_2189, retro_cjac_2896, retro_cjac_300, retro_cjac_3181, retro_cjac_3311, retro_cjac_3335, retro_cjac_390,
Ciona savignyi	ENSCSAVG00000007011	1 retrocopy	retro_csav_2,
Ficedula albicollis	ENSFALG00000001088	1 retrocopy	retro_falb_2,
Gallus gallus	ENSGALG00000005393	1 retrocopy	retro_ggal_7,
Latimeria chalumnae	ENSLACG00000019009	1 retrocopy	retro_lcha_10,
Myotis lucifugus	ENSMLUG00000007020	6 retrocopies	retro_mluc_1631, retro_mluc_242, retro_mluc_2605, retro_mluc_428, retro_mluc_511, retro_mluc_876,
Macaca mulatta	ENSMMUG00000002792	3 retrocopies	retro_mmul_237, retro_mmul_541, retro_mmul_810,
Oryctolagus cuniculus	ENSOCUG00000023645	2 retrocopies	retro_ocun_1137, retro_ocun_247,
Otolemur garnettii	ENSOGAG00000010974	4 retrocopies	retro_ogar_2431, retro_ogar_295, retro_ogar_3353, retro_ogar_974,
Procavia capensis	ENSPCAG00000014202	2 retrocopies	retro_pcap_15, retro_pcap_23,
Pongo abelii	ENSPPYG00000000148	3 retrocopies	retro_pabe_3159, retro_pabe_849, retro_pabe_965,
Pelodiscus sinensis	ENSPSIG00000009767	1 retrocopy	retro_psin_12,
Sarcophilus harrisii	ENSSHAG00000014599	3 retrocopies	retro_shar_106, retro_shar_462, retro_shar_725,
Ictidomys tridecemlineatus	ENSSTOG00000009288	3 retrocopies	retro_itri_1754, retro_itri_273, retro_itri_363,
Taeniopygia guttata	ENSTGUG00000000233	1 retrocopy	retro_tgut_2,
Tetraodon nigroviridis	ENSTNIG00000011685	1 retrocopy	retro_tnig_19,
Vicugna pacos	ENSVPAG00000003224	4 retrocopies	retro_vpac_281, retro_vpac_328, retro_vpac_6, retro_vpac_78,