RetrogeneDB ID: retro_btau_175

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 11:68383812..68384883(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000008985
• Aliases: PCBP1, hnRNP-E1
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: PCBP2
• Ensembl ID: ENSBTAG00000020757
• Aliases: None
• Description: poly(rC)-binding protein 2 [Source:RefSeq peptide;Acc:NP_001029883]

Sequence

>retro_btau_175
ATGGATGCCGGTGTGACTGAAAGTGGACTAAATGTGACTCTCACCATTCGGCTGCTTATGCACGGAAAGGAAGTAGGAAG
CATCATTGGGAAGAAAGGGGAGTCGGTTAAGAGGATCCGCGAGGAGAGTGGCGCGCGGATCAACATCTCGGAGGGGAATT
GCCCGGAGAGAATCATCACTCTGACCGGCCCCACCAATGCCATCTTTAAGGCCTTCGCTATGATTATCGACAAGCTGGAA
GAAGATATCAACAGCTCCATGACCAACAGCACGGCGGCCAGCAGGCCCCCGGTCACCCTGAGGCTGGTGGTGCCGGCCAC
CCAGTGCGGCTCCCTGATTGGGAAAGGCGGGTGTAAGATCAAAGAGATCCGCGAGAGTACCGGGGCCCAGGTCCAGGTGG
CGGGGGATATGCTGCCCAACTCCACCGAGCGGGCCATCACCATTGCTGGCGTGCCGCAGTCTGTCACCGAGTGTGTCAAG
CAGATCTGCCTGGTCATGCTGGAGACGCTCTCCCAGTCTCCGCAAGGGAGAGTCATGACCATTCCGTACCAGCCCATGCC
GGCCAGCTCTCCAGTCATCTGCGCGGGCGGCCAAGATCGGTGCAGCGACGCTGCGGGCTACCCCCACGCCACCCATGACC
TGGAGGGACCACCTCTAGATGCCTACTCGATTCAAGGACAACACACCATTTCTCCGCTCGATCTGGCCAAGCTGAACCAG
GTGGCAAGACAACAGTCTCACTTTGCCATGATGCACGGCGGGACCGGATTCGCCGGAATTGACTCCAGCTCTCCAGAGGT
GAAAGGCTATTGGGCAAGTTTGGATGCATCTACTCAAACCACCCATGAACTCACCATTCCAAATAACTTAATTGGCTGCA
TAATCGGGCGCCAAGGCGCCAACATTAATGAGATCCGCCAGATGTCCGGGGCCCAGATCAAAATTGCCAACCCAGTGGAA
GGCTCTTCTGGTAGGCAGGTTACTATCACTGGTTCTGCTGCCAGTATTAGTCTGGCCCAATATCTAATCAATGCCAGGCT
TTCTTCTGAGAAGGGCATGGGGTGCAGCTAG

Alignment

ORF - retro_btau_175 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.58 %
• Parental protein coverage: 59.89 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDTGVIEGGLNVTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNCPERIITLAGPTNAIFK
          MD.GV.E.GLNVTLTIRLLMHGKEVGSIIGKKGESVK..REESGARINISEGNCPERIITL.GPTNAIFK
Retrocopy MDAGVTESGLNVTLTIRLLMHGKEVGSIIGKKGESVKRIREESGARINISEGNCPERIITLTGPTNAIFK

Parental  AFAMIIDKLEEDISSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPN
          AFAMIIDKLEEDI.SSMTNSTAASRPPVTLRLVVPA.QCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPN
Retrocopy AFAMIIDKLEEDINSSMTNSTAASRPPVTLRLVVPATQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPN

Parental  STERAITIAGIPQSIIECVKQICVVMLES---PPKG--VTIPYRPKPSSSPVIFAGGQDRYSTGSDSASF
          STERAITIAG.PQS..ECVKQIC.VMLE.....P.G...TIPY.P.P.SSPVI.AGGQDR.S...D.A..
Retrocopy STERAITIAGVPQSVTECVKQICLVMLETLSQSPQGRVMTIPYQPMPASSPVICAGGQDRCS---DAAGY

Parental  PHTT
          PH.T
Retrocopy PHAT

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	47.29 RPM	121.19 RPM
ERP005899_muscle	132.24 RPM	321.75 RPM
SRP017611_brain	86.01 RPM	165.86 RPM
SRP017611_kidney	156.83 RPM	350.77 RPM
SRP017611_liver	129.42 RPM	198.74 RPM
SRP030211_testis	78.60 RPM	380.65 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

7 EST(s) were mapped to retro_btau_175 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
AV662360	68383911	68384332	100	421	0	421
BE483319	68383792	68384308	100	516	0	516
CF765515	68383775	68384368	99.7	591	2	589
DY043769	68383751	68384118	100	367	0	367
DY178137	68384182	68384371	100	189	0	189
DY201713	68384003	68384388	99.3	382	3	379
EE942063	68384109	68384440	100	331	0	331

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_175 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_175 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Sus scrofa	retro_sscr_61
Equus caballus	retro_ecab_67
Pongo abelii	retro_pabe_92
Oryctolagus cuniculus	retro_ocun_10

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Parental genes homology:

Parental genes homology involve 24 parental genes, and 53 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020757	1 retrocopy	retro_btau_175 ,
Bos taurus	ENSBTAG00000021131	2 retrocopies	retro_btau_468, retro_btau_605,
Canis familiaris	ENSCAFG00000006821	1 retrocopy	retro_cfam_54,
Callithrix jacchus	ENSCJAG00000018590	2 retrocopies	retro_cjac_3253, retro_cjac_754,
Cavia porcellus	ENSCPOG00000000967	2 retrocopies	retro_cpor_193, retro_cpor_97,
Dasypus novemcinctus	ENSDNOG00000008688	6 retrocopies	retro_dnov_1146, retro_dnov_1399, retro_dnov_1672, retro_dnov_1823, retro_dnov_2434, retro_dnov_452,
Equus caballus	ENSECAG00000022389	1 retrocopy	retro_ecab_67,
Echinops telfairi	ENSETEG00000014741	3 retrocopies	retro_etel_1170, retro_etel_2108, retro_etel_840,
Homo sapiens	ENSG00000197111	2 retrocopies	retro_hsap_4077, retro_hsap_83,
Gorilla gorilla	ENSGGOG00000012613	2 retrocopies	retro_ggor_212, retro_ggor_2734,
Macropus eugenii	ENSMEUG00000001887	7 retrocopies	retro_meug_1143, retro_meug_1988, retro_meug_432, retro_meug_526, retro_meug_618, retro_meug_828, retro_meug_964,
Microcebus murinus	ENSMICG00000011651	2 retrocopies	retro_mmur_1226, retro_mmur_1228,
Myotis lucifugus	ENSMLUG00000009971	3 retrocopies	retro_mluc_2199, retro_mluc_314, retro_mluc_571,
Macaca mulatta	ENSMMUG00000006608	2 retrocopies	retro_mmul_1263, retro_mmul_1994,
Mus musculus	ENSMUSG00000056851	1 retrocopy	retro_mmus_274,
Nomascus leucogenys	ENSNLEG00000017693	1 retrocopy	retro_nleu_10,
Oryctolagus cuniculus	ENSOCUG00000022490	3 retrocopies	retro_ocun_10, retro_ocun_1622, retro_ocun_898,
Pongo abelii	ENSPPYG00000004581	2 retrocopies	retro_pabe_3346, retro_pabe_92,
Pan troglodytes	ENSPTRG00000005018	1 retrocopy	retro_ptro_113,
Pteropus vampyrus	ENSPVAG00000012284	3 retrocopies	retro_pvam_1168, retro_pvam_1369, retro_pvam_868,
Rattus norvegicus	ENSRNOG00000036852	2 retrocopies	retro_rnor_1238, retro_rnor_2088,
Sus scrofa	ENSSSCG00000000274	1 retrocopy	retro_sscr_61,
Ictidomys tridecemlineatus	ENSSTOG00000003635	2 retrocopies	retro_itri_1522, retro_itri_557,
Vicugna pacos	ENSVPAG00000000406	1 retrocopy	retro_vpac_471,