RetrogeneDB ID: retro_btau_1138

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 28:5837110..5837603(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C11H9ORF78
• Ensembl ID: ENSBTAG00000020307
• Aliases: None
• Description: None

Sequence

>retro_btau_1138
ATGAAAACAGGAGGTGTGGAAGACATAAGGAAGCTGAAGAACAGAGCCACAGAAGAGATCAGTGAACAGAAAGACCCCAC
TTGAACATGTTTTTGCAAAGAAACCAACCAAAGGCATGCGATCACGCACATGATGAAGAGCTTTGAGACAGAGCTGAAGA
AAAGGAAAGGGATAGAGATCATGGAAGCAGAAAGTCAAGCTGAAGAATGTAATCTTGTGAACTTTCAGAAAGCATCCTCA
GCAAAGACAGTGGGGATATCTCCTAATTGGATGTTAAGTAGCGTGCCCAAGGTGAACCTCCACATGATGCTGCAATGAAA
CATATTTCCATGGAGAATGCTAAGGCCCATCTGCTGGAAGATCAGCAGAACAAGAAGAAAGACAGTGAGACATCCTCTAC
CTTCACCAACATGTGTGAATTATAAGCAGTACATGGATCTTATCACAGTGTACTCAATGCCCCCAGATGGAGAATAAAGA
AGAGCCCAAGGCC

Alignment

ORF - retro_btau_1138 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.85 %
• Parental protein coverage: 66.04 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MKTGGMVDMKKLKERGKDKISEEEDLHLGTSFSAETNRRDEDADMMKYIETELKKRKGIVEHEEQKVKPK
          MKTGG..D..KLK.R....ISE..D....T.F..ETN.R.....MMK..ETELKKRKGI...E.......
Retrocopy MKTGGVEDIRKLKNRATEEISEQKD-PT*TCFCKETNQRHAITHMMKSFETELKKRKGIEIMEAE----S

Parental  NAEDCLYELPENIRVSSAKKTEEMLSNQMLSGIPEVDLGI-DAKIKNIISTEDAKARLLAEQQNKKKDSE
          .AE.C...L......SSA.KT.....N.MLS..P.V.L...DA..K..IS.E.AKA.LL..QQNKKKDSE
Retrocopy QAEEC--NLVNFQKASSA-KTVGISPNWMLSSVPKVNLHM<DAAMKH-ISMENAKAHLLEDQQNKKKDSE

Parental  TSFVPTNMAVNYVQHNRFYHEELNAPIRR-NKEEPKA
          TS...TNM......H...YH..LNAP..R.NKEEPKA
Retrocopy TSSTFTNMCEL*AVHGS-YHSVLNAPRWR<NKEEPKA

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	17.45 RPM
ERP005899_muscle	0.00 RPM	20.80 RPM
SRP017611_brain	0.00 RPM	28.28 RPM
SRP017611_kidney	0.00 RPM	31.95 RPM
SRP017611_liver	0.00 RPM	15.18 RPM
SRP030211_testis	0.02 RPM	26.07 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1138 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1138 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1138 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_320
Pan troglodytes	retro_ptro_258
Callithrix jacchus	retro_cjac_1757
Equus caballus	retro_ecab_174

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020307	1 retrocopy	retro_btau_1138 ,
Canis familiaris	ENSCAFG00000019979	1 retrocopy	retro_cfam_116,
Choloepus hoffmanni	ENSCHOG00000013895	3 retrocopies	retro_chof_1103, retro_chof_1747, retro_chof_978,
Cavia porcellus	ENSCPOG00000009285	1 retrocopy	retro_cpor_712,
Equus caballus	ENSECAG00000018958	1 retrocopy	retro_ecab_174,
Gorilla gorilla	ENSGGOG00000013358	1 retrocopy	retro_ggor_1990,
Macropus eugenii	ENSMEUG00000010524	3 retrocopies	retro_meug_1046, retro_meug_1241, retro_meug_508,
Microcebus murinus	ENSMICG00000009596	1 retrocopy	retro_mmur_1466,
Monodelphis domestica	ENSMODG00000006832	1 retrocopy	retro_mdom_518,
Mus musculus	ENSMUSG00000026851	1 retrocopy	retro_mmus_2978,
Otolemur garnettii	ENSOGAG00000009770	1 retrocopy	retro_ogar_1015,
Pongo abelii	ENSPPYG00000019685	1 retrocopy	retro_pabe_2426,
Sarcophilus harrisii	ENSSHAG00000012313	1 retrocopy	retro_shar_746,
Ictidomys tridecemlineatus	ENSSTOG00000020630	1 retrocopy	retro_itri_1783,
Tupaia belangeri	ENSTBEG00000013115	1 retrocopy	retro_tbel_514,