RetrogeneDB ID: retro_btau_131

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 14:58850397..58850958(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000006213
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: IFT27
• Ensembl ID: ENSBTAG00000026657
• Aliases: IFT27, RABL4
• Description: Intraflagellar transport protein 27 homolog [Source:UniProtKB/Swiss-Prot;Acc:Q0VCN3]

Sequence

>retro_btau_131
ATGGTGAAGCTCGCAGCCAAATGCATCCTGGCAGGAGACCCCACCGTGGGCAAGACCGCCCTGGCACAGCTCTTCCACAG
CGACGGGGCCCATTTCCAGAAGAACTACACCCTGACAACAGGGGTGGATCTGGTGGTGAAAACAGTGGCAGTCCCTGACA
CGGGGGACAGTGTGGAACTCTTCATTTTTGACTCGGCCGGCAAAGAGCTGTTTTCTGAAATGCTGGATAAACTGTGGGAG
AGTCCCAATGTCTTGTGTCTTGTCTACGACGTGACCAACGAGCAGTCCTTCACCAACTGCAGCAAGTGGCTGGAGAAGGC
TCGGTCTCAGATTCCAGGGACCACCCTCCCAGGTGTGCTAGTGGGAAACAAGACAGACCTGGCTGGCAGGCGAGTGGTGG
ATGTGGCCCAGGCCCAGGCGTGGGCACTGGGCCAAGGCCTGGAATGTTTTGAAACATCCGTGAAGGAGATGGAAAACTAT
GAAGCCCCTTTCCACTACCTGGCCAAGCAGTTTCACCACCTGTACCGGGAGAAGCTGGAGGTTTTCCAGGTGCTGGTGTG
A

Alignment

ORF - retro_btau_131 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.39 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVKLAAKCILAGDPTVGKTALAQLFRSDGAHFQKNYTLTTGVDLVVKTVPVPDTGDSVELFIFDSAGKEL
          MVKLAAKCILAGDPTVGKTALAQLF.SDGAHFQKNYTLTTGVDLVVKTV.VPDTGDSVELFIFDSAGKEL
Retrocopy MVKLAAKCILAGDPTVGKTALAQLFHSDGAHFQKNYTLTTGVDLVVKTVAVPDTGDSVELFIFDSAGKEL

Parental  FSEMLDKLWESPNVLCLVYDVTNEQSFTNCSKWLEKARSQIPGTTLPGVLVGNKTDLAGRRVVDVAQAQA
          FSEMLDKLWESPNVLCLVYDVTNEQSFTNCSKWLEKARSQIPGTTLPGVLVGNKTDLAGRRVVDVAQAQA
Retrocopy FSEMLDKLWESPNVLCLVYDVTNEQSFTNCSKWLEKARSQIPGTTLPGVLVGNKTDLAGRRVVDVAQAQA

Parental  WALGQGLECFETSVKEMENYEAPFHYLAKQFHHLYREKLEVFQALV
          WALGQGLECFETSVKEMENYEAPFHYLAKQFHHLYREKLEVFQ.LV
Retrocopy WALGQGLECFETSVKEMENYEAPFHYLAKQFHHLYREKLEVFQVLV

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	0.65 RPM
ERP005899_muscle	0.00 RPM	3.11 RPM
SRP017611_brain	0.27 RPM	8.41 RPM
SRP017611_kidney	0.36 RPM	5.93 RPM
SRP017611_liver	0.00 RPM	1.06 RPM
SRP030211_testis	3.12 RPM	57.86 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_131 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_131 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_131 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000026657	1 retrocopy	retro_btau_131 ,
Callithrix jacchus	ENSCJAG00000013961	1 retrocopy	retro_cjac_1566,