RetrogeneDB ID: retro_btau_1737

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: X:38597969..38599157(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000022128
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: OLA1
• Ensembl ID: ENSBTAG00000006970
• Aliases: None
• Description: Obg-like ATPase 1 [Source:UniProtKB/Swiss-Prot;Acc:Q2HJ33]

Sequence

>retro_btau_1737
ATGCCCCCCAAAAAGGGAGGTGATGGAATTAAACCACCCCCAATCATTGGAAGATTTGGAACCTCCTTGAAAATTGGTAT
TGTTGGATTACCAAATGTTGGGAAATCTACCTTCTTCAATGTACTAACCAATAGTCAAGCTTCAGCAGAAAACTTCCCAT
TCTGCACTATTGATCCGAATGAGAGCAGAGTACCTGTGCCTGATGAAAGATTTGACTTTCTTTGCCAGTACCACAAACCA
GCAAGCAAAATTCCTGCTTTTCTAAATGTAGTGGATATTGCTGGCCTTGTGAAAGGAGCTCACAATGGGCAAGGCCTGGG
GAATGCCTTTTTATCTCATATTAGTGCCTGTGATGGAATCTTTCATTTAACACGTGCTTTTGAAGATGATGATATCACAC
ATGTTGAAGGAAGTGTAGATCCTGTTCGAGATATAGAAATAATACATGAAGAGCTTCAGCTTAAAGATGAGGAAATGGTT
GGGCCCATTATAGATAAACTAGAGAAAGTGGCTGTGAGAGGTGGAGATAAAAAACTAAAACCTGAATATGACATAATGTG
CAAAGTCAAATCCTGGGTTATAGATCAAAAGAAACCTGTTCGATTCTATCATGATTGGAATGACAAAGAGATTGAAGTAT
TGAATAAACACTTATTTCTGACTTCAAAACCAATGGTCTACTTGGTTAATCTTTCCGAAAAAGACTACATTAGAAAGAAA
AACAAATGGTTGATAAAAATTAAAGAGTGGGTGGACAAGTATGACCCAAGTGCCTTGGTCATTCCTTTTAGTGGGGCCTT
GGAACTCAGGTTGCAAGAATTGAGTGCTGAGGAGAGACAGAAGTATCTGGAAGCGAACATGACACAAAGCGCTTTGCCAA
AGATCATTAAGGCTGGGTTTGCAGCACTCCAACTAGAATACTTTTTCACTGCAGGCCCAGATGAAGTGCGTGCATGGACC
ATCAGGAAAGGGACGAAGGCTCCTCAAGCTGCAGGAAAGATTCACACAGATTTTGAAAAAGGATTCATTATGGCTGAAGT
AATGAAATACGAAGATTTTAAAGAGGAAGGTTCTGAAAATGCAGTCAAGGCTGCTGGAAAGTACAGACAACAAGGCAGAA
ATTATATTGTTGAAGATGGAGATATTATCTTCTTCAAATTTAATACACCTCAGCAACCGAAGAAGAAA

Alignment

ORF - retro_btau_1737 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.75 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPPKKGGDGIKPPPIIGRFGTSLKIGIVGLPNVGKSTFFNVLTNSQASAENFPFCTIDPNESRVPVPDER
          MPPKKGGDGIKPPPIIGRFGTSLKIGIVGLPNVGKSTFFNVLTNSQASAENFPFCTIDPNESRVPVPDER
Retrocopy MPPKKGGDGIKPPPIIGRFGTSLKIGIVGLPNVGKSTFFNVLTNSQASAENFPFCTIDPNESRVPVPDER

Parental  FDFLCQYHKPASKIPAFLNVVDIAGLVKGAHNGQGLGNAFLSHISACDGIFHLTRAFEDDDITHVEGSVD
          FDFLCQYHKPASKIPAFLNVVDIAGLVKGAHNGQGLGNAFLSHISACDGIFHLTRAFEDDDITHVEGSVD
Retrocopy FDFLCQYHKPASKIPAFLNVVDIAGLVKGAHNGQGLGNAFLSHISACDGIFHLTRAFEDDDITHVEGSVD

Parental  PVRDIEIIHEELQLKDEEMVGPIIDKLEKVAVRGGDKKLKPEYDIMCKVKSWVIDQKKPVRFYHDWNDKE
          PVRDIEIIHEELQLKDEEMVGPIIDKLEKVAVRGGDKKLKPEYDIMCKVKSWVIDQKKPVRFYHDWNDKE
Retrocopy PVRDIEIIHEELQLKDEEMVGPIIDKLEKVAVRGGDKKLKPEYDIMCKVKSWVIDQKKPVRFYHDWNDKE

Parental  IEVLNKHLFLTSKPMVYLVNLSEKDYIRKKNKWLIKIKEWVDKYDPGALVIPFSGALELRLQELSAEERQ
          IEVLNKHLFLTSKPMVYLVNLSEKDYIRKKNKWLIKIKEWVDKYDP.ALVIPFSGALELRLQELSAEERQ
Retrocopy IEVLNKHLFLTSKPMVYLVNLSEKDYIRKKNKWLIKIKEWVDKYDPSALVIPFSGALELRLQELSAEERQ

Parental  KYLEANMTQSALPKIIKAGFAALQLEYFFTAGPDEVRAWTIRKGTKAPQAAGKIHTDFEKGFIMAEVMKY
          KYLEANMTQSALPKIIKAGFAALQLEYFFTAGPDEVRAWTIRKGTKAPQAAGKIHTDFEKGFIMAEVMKY
Retrocopy KYLEANMTQSALPKIIKAGFAALQLEYFFTAGPDEVRAWTIRKGTKAPQAAGKIHTDFEKGFIMAEVMKY

Parental  EDFKEEGSENAVKAAGKYRQQGRNYIVEDGDIIFFKFNTPQQPKKK
          EDFKEEGSENAVKAAGKYRQQGRNYIVEDGDIIFFKFNTPQQPKKK
Retrocopy EDFKEEGSENAVKAAGKYRQQGRNYIVEDGDIIFFKFNTPQQPKKK

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	4.90 RPM	14.78 RPM
ERP005899_muscle	3.22 RPM	37.53 RPM
SRP017611_brain	5.21 RPM	13.06 RPM
SRP017611_kidney	5.63 RPM	14.64 RPM
SRP017611_liver	2.72 RPM	11.48 RPM
SRP030211_testis	2.43 RPM	44.15 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

3 EST(s) were mapped to retro_btau_1737 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
AF071901	38597979	38598168	100	175	0	174
AF107886	38597979	38598142	100	163	0	163
DY212719	38598248	38598630	100	382	0	382

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1737 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1737 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006970	1 retrocopy	retro_btau_1737 ,
Choloepus hoffmanni	ENSCHOG00000005044	1 retrocopy	retro_chof_1295,
Callithrix jacchus	ENSCJAG00000007877	1 retrocopy	retro_cjac_2875,
Dipodomys ordii	ENSDORG00000008681	1 retrocopy	retro_dord_556,
Homo sapiens	ENSG00000138430	1 retrocopy	retro_hsap_2593,
Gorilla gorilla	ENSGGOG00000022215	1 retrocopy	retro_ggor_1623,
Myotis lucifugus	ENSMLUG00000025196	1 retrocopy	retro_mluc_626,
Monodelphis domestica	ENSMODG00000009296	1 retrocopy	retro_mdom_1428,
Nomascus leucogenys	ENSNLEG00000005817	1 retrocopy	retro_nleu_1526,
Otolemur garnettii	ENSOGAG00000016557	1 retrocopy	retro_ogar_1697,
Pongo abelii	ENSPPYG00000012943	2 retrocopies	retro_pabe_1912, retro_pabe_928,
Pan troglodytes	ENSPTRG00000012650	1 retrocopy	retro_ptro_1517,
Sorex araneus	ENSSARG00000010743	1 retrocopy	retro_sara_545,
Tarsius syrichta	ENSTSYG00000005517	2 retrocopies	retro_tsyr_1845, retro_tsyr_394,
Vicugna pacos	ENSVPAG00000009660	2 retrocopies	retro_vpac_52, retro_vpac_613,