RetrogeneDB ID: retro_btau_1283

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 3:71025191..71025906(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000006473
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RNPS1
• Ensembl ID: ENSBTAG00000009969
• Aliases: None
• Description: RNA-binding protein with serine-rich domain 1 [Source:UniProtKB/Swiss-Prot;Acc:A6QR16]

Sequence

>retro_btau_1283
AAAGAGAATTTGCTAGGAGTCAAAGAAAATAATAAAATGTCCAGCACTAGAGCTCCCGCTCCTTCTCCTACCAAATGCAA
AGATCACTCTGATAAAACTCCAAGGATCGCTCTAGAGATAAAGTGACCACCAAGGAGTCAGGAGAGAAGGATCATGACTG
GTGTGAAACTCAAAAGTGGTGCAATGCTTCCAGTGGTAGCAGCAGCACCAGGTCTCAGTTGGCTCCATCTCTAGTTCGGG
CCCCAGAACGGGCTCCAGCAGCAGCTCCAGCTCATCCTCAGCATCCAGCCTCTCAGAAGTTGCAGCATATCCTGCAGCTC
CAGCTCCAGCAGCACCTCTGGCTCTCAGAGTCCTTCTCAGGGCAAATATGACAATAGGTAGGGCTCCCCCTCCAAATTCA
AACCTCCCAAAAAAGATGAAAACAAAAAGAAAAGGCAGAGACCTTCCCCCAAACCCACCAAAGTGCACATCAGGAGGCTC
ACCATGAATGTGACCAAGGATCACATCATGAAGCTACACTCCAACTCTGGGAAAATTAATGATTGACATGTCTGTGGAAA
GGATGCAGCCCCATCTGTCTAAAGACAACACATGTATGGAGTTTGAGAATCCAGATGAGGTGGAAAAGGCACTGAAGCAC
ATGGATGGAGGACAAATTGATGGTCAGAAGAGCACTGCCAACGCTGTGCTGGCCCTCTGGCCTCGGCCAGCTCCA

Alignment

ORF - retro_btau_1283 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.67 %
• Parental protein coverage: 78.69 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  KKSLLGVKENNKKSSTRAP--SPTKRKDRSDE-KSKDRSKDKGATKESSEKDRGRDKTRKRRSASSGSSS
          K..LLGVKENNK.SSTRAP..SPTK.KD.SD...SKDRS.DK..TKES.EKD.....T.K...ASSGSSS
Retrocopy KENLLGVKENNKMSSTRAPAPSPTKCKDHSDK<NSKDRSRDKVTTKESGEKDHDWCETQKWCNASSGSSS

Parental  TRSRSS-STSSSGSSTSTGSSSGSSSSSASSRSG-SSSTSRSSSSSSSSGSPSPSRRRHDNRRRSRSKSK
          TRS....S.SSSG..T..GSSS.SSSSSASS.S..S.S.S.SSSSSS.SGS.SPS....DNR..S.SK.K
Retrocopy TRSQLA<SISSSGPRT--GSSSSSSSSSASSLSE<SCSISCSSSSSSTSGSQSPSQGKYDNR*GSPSKFK

Parental  PPKRDEKERKRRSPSPKPTKVHIGRLTRNVTKDHIMEIFS-TYGKIKMIDMPVERMHPHLSKGYAYVEFE
          PP...........PSPKPTKVHI.RLT.NVTKDHIM...S.T.GK..MIDM.VERM.PHLSK.....EFE
Retrocopy PPXXXXXXXXXQRPSPKPTKVHIRRLTMNVTKDHIMKLHS>TLGKL-MIDMSVERMQPHLSKDNTCMEFE

Parental  NPDEAEKALKHMDGGQIDGQEITATAVLAPWPRPPP
          NPDE.EKALKHMDGGQIDGQ..TA.AVLA.WPRP.P
Retrocopy NPDEVEKALKHMDGGQIDGQKSTANAVLALWPRPAP

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	38.07 RPM
ERP005899_muscle	0.00 RPM	64.03 RPM
SRP017611_brain	0.00 RPM	71.76 RPM
SRP017611_kidney	0.00 RPM	66.62 RPM
SRP017611_liver	0.00 RPM	43.49 RPM
SRP030211_testis	0.07 RPM	81.86 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1283 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1283 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1283 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 43 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017861	1 retrocopy	retro_amel_194,
Bos taurus	ENSBTAG00000009969	7 retrocopies	retro_btau_1187, retro_btau_1239, retro_btau_1283 , retro_btau_1515, retro_btau_764, retro_btau_776, retro_btau_85,
Canis familiaris	ENSCAFG00000019397	1 retrocopy	retro_cfam_449,
Equus caballus	ENSECAG00000023288	1 retrocopy	retro_ecab_524,
Felis catus	ENSFCAG00000007690	1 retrocopy	retro_fcat_248,
Homo sapiens	ENSG00000205937	1 retrocopy	retro_hsap_2911,
Gorilla gorilla	ENSGGOG00000014275	1 retrocopy	retro_ggor_2016,
Macropus eugenii	ENSMEUG00000008882	1 retrocopy	retro_meug_1996,
Myotis lucifugus	ENSMLUG00000016808	3 retrocopies	retro_mluc_2237, retro_mluc_2618, retro_mluc_643,
Macaca mulatta	ENSMMUG00000019238	1 retrocopy	retro_mmul_794,
Monodelphis domestica	ENSMODG00000015891	1 retrocopy	retro_mdom_1171,
Mus musculus	ENSMUSG00000034681	1 retrocopy	retro_mmus_173,
Otolemur garnettii	ENSOGAG00000031582	1 retrocopy	retro_ogar_3241,
Rattus norvegicus	ENSRNOG00000008703	4 retrocopies	retro_rnor_1537, retro_rnor_2135, retro_rnor_2988, retro_rnor_649,
Sarcophilus harrisii	ENSSHAG00000016951	1 retrocopy	retro_shar_390,
Ictidomys tridecemlineatus	ENSSTOG00000013200	1 retrocopy	retro_itri_1160,
Tupaia belangeri	ENSTBEG00000009098	8 retrocopies	retro_tbel_1262, retro_tbel_1851, retro_tbel_2132, retro_tbel_2154, retro_tbel_2216, retro_tbel_3193, retro_tbel_3286, retro_tbel_4688,
Tarsius syrichta	ENSTSYG00000001629	1 retrocopy	retro_tsyr_957,
Tursiops truncatus	ENSTTRG00000008220	7 retrocopies	retro_ttru_1010, retro_ttru_1033, retro_ttru_1558, retro_ttru_1808, retro_ttru_1809, retro_ttru_203, retro_ttru_986,