RetrogeneDB ID: retro_btau_1084

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 25:13770849..13771359(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HNRPC
• Ensembl ID: ENSBTAG00000011396
• Aliases: LOC510852, HNRNPC, HNRPC
• Description: heterogeneous nuclear ribonucleoproteins C1/C2 [Source:RefSeq peptide;Acc:NP_001029567]

Sequence

>retro_btau_1084
TCTTTTGACTTGGACTGTGACTTTCAACAGGATTATTACGACAGGACGCACAGTTACCTAGCACGTGTTCCTCCTCCTCC
TCCTATTGCTCGGGCTGTAGTGCCCTCAGAACGCCAGCAGATATCAGGAAACACCTCATAAAAGGGCAAACATGGCTTCA
ATTCTAAGAGCAGACAGTAGGGATCTCCCTCTAAGTCTGGAAAGTTGAAAGGAGATGACCTTCAGACCATTAAGAAGGAG
TTAACTCAGATAAAACAAAAAGTGGGTTCTTTACTGGAAAGCCTGGGAAATAATTGAAAAGGAACGGAGCACACAAGGAG
TGGAGATAAAGAAGGGTAAGTCAGAAGAGGAGCAGAGCGGCAGCTCCCTGAGCAAGATGAGACTAATGAAGATGGAGTCT
GAGCCGGGGGTGCAGATGACTCTGCTGAGGAGGGGGACCTACTGGATGATGACGATAGTGAAGATCGGGGGGATGACCAG
CTGGAGTTGATCAAGGATGCTGAAACAGAG

Alignment

ORF - retro_btau_1084 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.23 %
• Parental protein coverage: 57.82 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SFDLDYDFQRDYYDRMYSYPARVPPPPPIARAVVPSKRQRVSGNTSRRGKSGFNSKSGQRGSSSKSGKLK
          SFDLD.DFQ.DYYDR..SY.ARVPPPPPIARAVVPS.RQ..SGNTS..GK.GFNSKS.Q.GS.SKSGKLK
Retrocopy SFDLDCDFQQDYYDRTHSYLARVPPPPPIARAVVPSERQQISGNTS*KGKHGFNSKSRQ*GSPSKSGKLK

Parental  GDDLQTIKKELTQIKQKVDSLLESL-EKIEKEQSKQGVEMKNDKSEEEQSSSSLKK-DETNVKMESEGGA
          GDDLQTIKKELTQIKQKV.SLLESL.E.IEKE.S.QGVE.K..KSEEEQS.SSL.K.DETN......GGA
Retrocopy GDDLQTIKKELTQIKQKVGSLLESL>EIIEKERSTQGVEIKKGKSEEEQSGSSLSK<DETNEDGV*AGGA

Parental  DDSAEEGDLLDDDDNEDRGDDQLELIKDDEKE
          DDSAEEGDLLDDDD.EDRGDDQLELIKD.E.E
Retrocopy DDSAEEGDLLDDDDSEDRGDDQLELIKDAETE

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	67.41 RPM
ERP005899_muscle	0.00 RPM	109.70 RPM
SRP017611_brain	0.14 RPM	94.65 RPM
SRP017611_kidney	0.00 RPM	118.84 RPM
SRP017611_liver	0.08 RPM	50.59 RPM
SRP030211_testis	0.09 RPM	112.53 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1084 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1084 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1084 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 36 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000011396	2 retrocopies	retro_btau_1084 , retro_btau_1142,
Canis familiaris	ENSCAFG00000005504	1 retrocopy	retro_cfam_1140,
Homo sapiens	ENSG00000092199	2 retrocopies	retro_hsap_1624, retro_hsap_3740,
Gorilla gorilla	ENSGGOG00000023015	1 retrocopy	retro_ggor_1046,
Macaca mulatta	ENSMMUG00000014809	4 retrocopies	retro_mmul_1112, retro_mmul_205, retro_mmul_468, retro_mmul_503,
Mustela putorius furo	ENSMPUG00000000164	2 retrocopies	retro_mputfur_231, retro_mputfur_241,
Nomascus leucogenys	ENSNLEG00000014362	2 retrocopies	retro_nleu_1828, retro_nleu_59,
Oryctolagus cuniculus	ENSOCUG00000015029	1 retrocopy	retro_ocun_138,
Otolemur garnettii	ENSOGAG00000012543	1 retrocopy	retro_ogar_165,
Pongo abelii	ENSPPYG00000005593	6 retrocopies	retro_pabe_1116, retro_pabe_1263, retro_pabe_1342, retro_pabe_2, retro_pabe_722, retro_pabe_780,
Pan troglodytes	ENSPTRG00000006118	2 retrocopies	retro_ptro_1089, retro_ptro_2539,
Rattus norvegicus	ENSRNOG00000011621	1 retrocopy	retro_rnor_922,
Tupaia belangeri	ENSTBEG00000011514	11 retrocopies	retro_tbel_1738, retro_tbel_2114, retro_tbel_2475, retro_tbel_2838, retro_tbel_2849, retro_tbel_3094, retro_tbel_3293, retro_tbel_3776, retro_tbel_3903, retro_tbel_3937, retro_tbel_818,