RetrogeneDB ID: retro_btau_765

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 19:44665684..44665918(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNRPF
• Ensembl ID: ENSBTAG00000016271
• Aliases: SNRPF, Sm-F, SmF, snRNP-F
• Description: Small nuclear ribonucleoprotein F [Source:UniProtKB/Swiss-Prot;Acc:Q3T0Z8]

Sequence

>retro_btau_765
ATGAGTTTGCCCCTCAACCCCAAACCTTTCCTCAACAGATCAACAGGAAAGCCAGTAATGGTGAAGCTTAAATGGGGAAT
GGAGTACAAAGGCTACCTTGTGCCTGTAGATGGCTATATGAACATGCAGCTTGCAAACACAGAAGAATACATAGATGGAG
CATTGTCTGGACATTTGGGTGAAGTTTTAATGAAGTGTAATAATGTCCTTTATATTAGGGGTGTTGAAGAAGAG

Alignment

ORF - retro_btau_765 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.59 %
• Parental protein coverage: 90.7 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSLPLNPKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYIDGALSGHLGEVLIRCNNVL
          MSLPLNPKPFLN..TGKPVMVKLKWGMEYKGYLV.VDGYMNMQLANTEEYIDGALSGHLGEVL..CNNVL
Retrocopy MSLPLNPKPFLNRSTGKPVMVKLKWGMEYKGYLVPVDGYMNMQLANTEEYIDGALSGHLGEVLMKCNNVL

Parental  YIRGVEEE
          YIRGVEEE
Retrocopy YIRGVEEE

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	1.30 RPM	19.18 RPM
ERP005899_muscle	0.16 RPM	26.98 RPM
SRP017611_brain	0.69 RPM	7.67 RPM
SRP017611_kidney	0.95 RPM	15.35 RPM
SRP017611_liver	0.15 RPM	8.91 RPM
SRP030211_testis	0.49 RPM	45.80 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_765 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_765 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_765 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 15 parental genes, and 37 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002166	3 retrocopies	retro_amel_1239, retro_amel_42, retro_amel_883,
Bos taurus	ENSBTAG00000014060	1 retrocopy	retro_btau_861,
Bos taurus	ENSBTAG00000016271	1 retrocopy	retro_btau_765 ,
Equus caballus	ENSECAG00000019817	1 retrocopy	retro_ecab_154,
Felis catus	ENSFCAG00000029966	4 retrocopies	retro_fcat_280, retro_fcat_66, retro_fcat_77, retro_fcat_861,
Homo sapiens	ENSG00000139343	3 retrocopies	retro_hsap_125, retro_hsap_2487, retro_hsap_2645,
Gorilla gorilla	ENSGGOG00000001127	2 retrocopies	retro_ggor_1549, retro_ggor_225,
Macaca mulatta	ENSMMUG00000009302	4 retrocopies	retro_mmul_1521, retro_mmul_361, retro_mmul_550, retro_mmul_893,
Mustela putorius furo	ENSMPUG00000007176	3 retrocopies	retro_mputfur_1309, retro_mputfur_377, retro_mputfur_941,
Mus musculus	ENSMUSG00000020018	4 retrocopies	retro_mmus_1060, retro_mmus_1197, retro_mmus_2537, retro_mmus_3210,
Nomascus leucogenys	ENSNLEG00000005835	3 retrocopies	retro_nleu_2259, retro_nleu_274, retro_nleu_651,
Pongo abelii	ENSPPYG00000004847	2 retrocopies	retro_pabe_381, retro_pabe_489,
Pteropus vampyrus	ENSPVAG00000009036	1 retrocopy	retro_pvam_1170,
Rattus norvegicus	ENSRNOG00000005556	4 retrocopies	retro_rnor_1822, retro_rnor_1849, retro_rnor_2926, retro_rnor_444,
Sus scrofa	ENSSSCG00000000895	1 retrocopy	retro_sscr_958,