RetrogeneDB ID: retro_btau_141

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 1:104146701..104147124(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000018312
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: PFN1
• Ensembl ID: ENSBTAG00000004915
• Aliases: None
• Description: Profilin-1 [Source:UniProtKB/Swiss-Prot;Acc:P02584]

Sequence

>retro_btau_141
ATGGCTGGGTGGAACGCCTACATCGACAACCTCATGGCGGACGGGACCTGTCAGGACGCAGCCATCGTGGGCTATAAGGA
CTCGCCCTCCGTCTGGGCCGCCGTCCCCGGCAAGACCTTCGTCAACATCACGCCTGCTGAGGTCGGTATCCTGGTTGGCA
AAGACCGGTCAAGTTTTTTCGTGAACGGGCTAACACTTGGGGGCCAGAAATGTTCTGTGATCCGGGACTCACTGCTGCAG
GATGGAGAATTTACCATGGATCTTCGTACCAAGAGCACCAGTGGAGCCCCAACCTTCAATATCACGGTCACCATGACTGC
CAAGACGCTAGTCCTGCTGATGGGCAAAGAAGGTGTCCATGGCGGTACGATCAACAAGAAATGTTATGAAATGGCTTCTC
ACCTGCGGCGTTCCCAGTACTGA

Alignment

ORF - retro_btau_141 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.57 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAGWNAYIDNLMADGTCQDAAIVGYKDSPSVWAAVPGKTFVNITPAEVGILVGKDRSSFFVNGLTLGGQK
          MAGWNAYIDNLMADGTCQDAAIVGYKDSPSVWAAVPGKTFVNITPAEVGILVGKDRSSFFVNGLTLGGQK
Retrocopy MAGWNAYIDNLMADGTCQDAAIVGYKDSPSVWAAVPGKTFVNITPAEVGILVGKDRSSFFVNGLTLGGQK

Parental  CSVIRDSLLQDGEFTMDLRTKSTGGAPTFNITVTMTAKTLVLLMGKEGVHGGMINKKCYEMASHLRRSQY
          CSVIRDSLLQDGEFTMDLRTKST.GAPTFNITVTMTAKTLVLLMGKEGVHGG.INKKCYEMASHLRRSQY
Retrocopy CSVIRDSLLQDGEFTMDLRTKSTSGAPTFNITVTMTAKTLVLLMGKEGVHGGTINKKCYEMASHLRRSQY

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	0.22 RPM	74.40 RPM
ERP005899_muscle	1.37 RPM	323.44 RPM
SRP017611_brain	0.14 RPM	45.36 RPM
SRP017611_kidney	0.12 RPM	92.05 RPM
SRP017611_liver	0.15 RPM	99.67 RPM
SRP030211_testis	0.17 RPM	32.99 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_141 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_141 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_141 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 45 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006193	2 retrocopies	retro_amel_1712, retro_amel_1781,
Bos taurus	ENSBTAG00000004915	1 retrocopy	retro_btau_141 ,
Callithrix jacchus	ENSCJAG00000011719	2 retrocopies	retro_cjac_1023, retro_cjac_1641,
Cavia porcellus	ENSCPOG00000013136	1 retrocopy	retro_cpor_1216,
Dasypus novemcinctus	ENSDNOG00000011649	2 retrocopies	retro_dnov_1762, retro_dnov_485,
Homo sapiens	ENSG00000108518	10 retrocopies	retro_hsap_214, retro_hsap_215, retro_hsap_221, retro_hsap_223, retro_hsap_224, retro_hsap_352, retro_hsap_446, retro_hsap_447, retro_hsap_450, retro_hsap_451,
Gorilla gorilla	ENSGGOG00000022394	3 retrocopies	retro_ggor_285, retro_ggor_289, retro_ggor_366,
Macaca mulatta	ENSMMUG00000002772	5 retrocopies	retro_mmul_407, retro_mmul_527, retro_mmul_528, retro_mmul_574, retro_mmul_732,
Mus musculus	ENSMUSG00000018293	1 retrocopy	retro_mmus_1326,
Nomascus leucogenys	ENSNLEG00000017446	6 retrocopies	retro_nleu_16, retro_nleu_1870, retro_nleu_2425, retro_nleu_2429, retro_nleu_848, retro_nleu_886,
Otolemur garnettii	ENSOGAG00000031395	3 retrocopies	retro_ogar_1680, retro_ogar_2143, retro_ogar_3351,
Procavia capensis	ENSPCAG00000000291	1 retrocopy	retro_pcap_27,
Pelodiscus sinensis	ENSPSIG00000004124	1 retrocopy	retro_psin_8,
Pan troglodytes	ENSPTRG00000008616	5 retrocopies	retro_ptro_185, retro_ptro_196, retro_ptro_276, retro_ptro_332, retro_ptro_333,
Rattus norvegicus	ENSRNOG00000003975	1 retrocopy	retro_rnor_1623,
Ictidomys tridecemlineatus	ENSSTOG00000028950	1 retrocopy	retro_itri_129,