RetrogeneDB ID: retro_btau_359

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 10:99483476..99484649(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PAIP1
• Ensembl ID: ENSBTAG00000020376
• Aliases: None
• Description: polyadenylate-binding protein-interacting protein 1 [Source:RefSeq peptide;Acc:NP_001098441]

Sequence

>retro_btau_359
GAACAAACGAGGCCCCTGAGAGCTCCATCTAGTTCGCCAGATAACATCCCACAGCAGAATTCGGAGTCAGCAATGGCTAA
AACCCAGGTGGTTGTAGCTCCTGTATTAATGTCTAAGCTGTCTGTAAACGCCCCTGAATTCTACGCATCAAGTTATTCTT
CTAATTATACAGAATCCTATGAGGACGGCTGTGAGGATTATCCTACTTTATCAGAATATGTTCAGGATTTTTTGAATCAT
CTTACAGAACAGCCTGGCAGTTTTTAAACTGAAATTGGACAGTTTGCAGAGACCCTGAATGGCTGGGTTACAACAGATGA
TGCTTTGCAAGAACTTATGGAACTCATCTATCAACAGGCCACATCTATCCCCAATTTCTCTTACATGGGAGCACGCCTCT
GTAACTACCTGTCCCATCATCTGACAATTAGCCCACAGAGTGGCAACTTTCGCCAATTGCTACTTCAAAGATGTCGGACT
GAATATGAAGTTAAAGATCAAGCTGCAAAAGGGGATGAAGTGACTCGAAAATGATTCCATGCATTTGTACTCTTTCTGGG
AGAACTCTATCTTAACCTGGAGATTAAAGGGACAAATGGACAGGTTACAAGGGCAGACATTCTTCAGACCGGTCTTCGGG
AGTTGCTGAATGCCCTCTTCTCTAATCCTATGGATGACAACTTAATCTGTGCAGCAAAATTACTGAAGTTGACAGGGTCA
GTTTTAGAAGATGCCTGGAAGGAAAAAGGAAAGACTGACATGGAAGAAATTATTCAGAGAATTGAAAATGTTGCCCTAGA
TGCAAATTGCAGCAGAGATGTAAAACAGATGCTTTTGAAGCTTGTAGAACTCCGGTCAAGTAACTGGGGTAGAGTCCATG
CAGCTTCAACATACAGGGAAGCAACACCTGAAAATGATCCTAATTATTTTATGAATGAGCCAACATTTTATACATCTGAT
GGTGTTCCTTTCACTGCAGCTGATCCAGATTACCAAGAGAAATATCAAGAGTTACTTGAAAGAGAAGACTTTTTTCCAGA
TTATGAAGAAAATGGAACAGATTTATCAGGGGGTGGTGATCCGTACTTGGATGATATTGATGATGAGATGGACCCAGAGA
TAGAAGAAGCTTATGAAAAGTTTTGTTTGGAATCAGAGCGTAAGCGAAAACAG

Alignment

ORF - retro_btau_359 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.47 %
• Parental protein coverage: 97.75 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EQTRPLRAPSSSPDNIPQQNSESAMAKPQVVVAPVLMSKLSVNAPEFYPSSYSSNYTESYEDGCEDYPTL
          EQTRPLRAPSSSPDNIPQQNSESAMAK.QVVVAPVLMSKLSVNAPEFY.SSYSSNYTESYEDGCEDYPTL
Retrocopy EQTRPLRAPSSSPDNIPQQNSESAMAKTQVVVAPVLMSKLSVNAPEFYASSYSSNYTESYEDGCEDYPTL

Parental  SEYVQDFLNHLTEQPGSFETEIGQFAETLNGWVTTDDALQELMELIYQQATSIPNFSYMGARLCNYLSHH
          SEYVQDFLNHLTEQPGSF.TEIGQFAETLNGWVTTDDALQELMELIYQQATSIPNFSYMGARLCNYLSHH
Retrocopy SEYVQDFLNHLTEQPGSF*TEIGQFAETLNGWVTTDDALQELMELIYQQATSIPNFSYMGARLCNYLSHH

Parental  LTISPQSGNFRQLLLQRCRTEYEVKDQAAKGDEVTRKRFHAFVLFLGELYLNLEIKGTNGQVTRADILQT
          LTISPQSGNFRQLLLQRCRTEYEVKDQAAKGDEVTRK.FHAFVLFLGELYLNLEIKGTNGQVTRADILQT
Retrocopy LTISPQSGNFRQLLLQRCRTEYEVKDQAAKGDEVTRK*FHAFVLFLGELYLNLEIKGTNGQVTRADILQT

Parental  GLRELLNALFSNPMDDNLICAVKLLKLTGSVLEDAWKEKGKTDMEEIIQRIENVVLDANCSRDVKQMLLK
          GLRELLNALFSNPMDDNLICA.KLLKLTGSVLEDAWKEKGKTDMEEIIQRIENV.LDANCSRDVKQMLLK
Retrocopy GLRELLNALFSNPMDDNLICAAKLLKLTGSVLEDAWKEKGKTDMEEIIQRIENVALDANCSRDVKQMLLK

Parental  LVELRSSNWGRVHAASTYREATPENDPNYFMNEPTFYTSDGVPFTAADPDYQEKYQELLEREDFFPDYEE
          LVELRSSNWGRVHAASTYREATPENDPNYFMNEPTFYTSDGVPFTAADPDYQEKYQELLEREDFFPDYEE
Retrocopy LVELRSSNWGRVHAASTYREATPENDPNYFMNEPTFYTSDGVPFTAADPDYQEKYQELLEREDFFPDYEE

Parental  NGTDLSGGGDPYLDDIDDEMDPEIEEAYEKFCLESERKRKQ
          NGTDLSGGGDPYLDDIDDEMDPEIEEAYEKFCLESERKRKQ
Retrocopy NGTDLSGGGDPYLDDIDDEMDPEIEEAYEKFCLESERKRKQ

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	0.07 RPM	29.92 RPM
ERP005899_muscle	0.11 RPM	39.22 RPM
SRP017611_brain	0.41 RPM	20.51 RPM
SRP017611_kidney	0.12 RPM	31.53 RPM
SRP017611_liver	0.08 RPM	15.71 RPM
SRP030211_testis	0.63 RPM	96.71 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_359 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_359 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_359 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020376	1 retrocopy	retro_btau_359 ,
Choloepus hoffmanni	ENSCHOG00000004961	1 retrocopy	retro_chof_762,
Callithrix jacchus	ENSCJAG00000001340	2 retrocopies	retro_cjac_3224, retro_cjac_3337,
Cavia porcellus	ENSCPOG00000002525	2 retrocopies	retro_cpor_133, retro_cpor_197,
Erinaceus europaeus	ENSEEUG00000009651	1 retrocopy	retro_eeur_304,
Homo sapiens	ENSG00000172239	1 retrocopy	retro_hsap_1726,
Otolemur garnettii	ENSOGAG00000001887	2 retrocopies	retro_ogar_1096, retro_ogar_1241,
Ochotona princeps	ENSOPRG00000000386	2 retrocopies	retro_opri_185, retro_opri_469,
Ictidomys tridecemlineatus	ENSSTOG00000011203	1 retrocopy	retro_itri_234,