RetrogeneDB ID: retro_tbel_4411

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_81516:3507..4164(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTBEG00000008179
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MRRF
• Ensembl ID: ENSTBEG00000016569
• Aliases: None
• Description: mitochondrial ribosome recycling factor [Source:HGNC Symbol;Acc:7234]

Sequence

>retro_tbel_4411
ATGGCCTTCGGCTTAAAGTGTTATCGCTTCCTCCACCCTGCCTTTTACAGTTACCTTGCAGCCTTGACCAGACCTGTTAC
AGAAATTACACCGAGAATAACGACTGGAAGACAGCCTGACCATAGGCAATTCGTGGCCTGTGCAGCTGTTCCAAGTCGCC
ATTTTGCCACCAAGAAAGCCAAAGCCAAATGGAAGGGACAGTCCCAAACTAGAATGAATATTAACACTGCCTTGGTTGAA
GATATAATCAACTTGGAAGAGGTTGATGAAGAAATGAAGTCTGTGATGGAAGCACTCAAGTATAATTTCAATAAGACTCT
CAATATAAGGACCTCTCCAGGATCCCTTGATCATATCACTGTGGTAACTGCTGATGGGAAACTTGCTTTAAACCAGATTA
GCCAGATCTCAATGAAGTCACCACAGCTGATTTTGTTGAATATGGCCAGCTTCCCAGAGTGTACAGCTGCAGCTATCAAG
GCTATAAGAGAAAGTGGAATGAATTTGAACCCAGAAGTGGAAGGGACGCTAATTCGGGTCCCCATTCTCAAAGCAACCAG
GGAACATAGGGAAATGCTGGTGAAACTGGCCAAACAGAACACAAACAAAACCAAAGACTCCTTACAAAAGGTTCACATCA
ACGCAATGAATAAGCTG

Alignment

ORF - retro_tbel_4411 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.24 %
• Parental protein coverage: 83.59 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAFGLKCYRLVHPAFRSYLAALTRPVTEVTPRIMNGRQPDHRQFVACAAVPSRHFATKKTKAKGKGQSQT
          MAFGLKCYR..HPAF.SYLAALTRPVTE.TPRI..GRQPDHRQFVACAAVPSRHFATKK.KAK.KGQSQT
Retrocopy MAFGLKCYRFLHPAFYSYLAALTRPVTEITPRITTGRQPDHRQFVACAAVPSRHFATKKAKAKWKGQSQT

Parental  RMNINTTLVEDIINLEEVDEEMKSVMEALKDNFNKTLNIRTSPGSLDHITVVTADGKLALNQISQISMKS
          RMNINT.LVEDIINLEEVDEEMKSVMEALK.NFNKTLNIRTSPGSLDHITVVTADGKLALNQISQISMKS
Retrocopy RMNINTALVEDIINLEEVDEEMKSVMEALKYNFNKTLNIRTSPGSLDHITVVTADGKLALNQISQISMKS

Parental  PQLILVNMASFPECTAAAIKAIRESGMNLNPEVEGTLIRVPIPKVTREHREMLVKLAKQNTNKAKDSLRK
          PQLIL.NMASFPECTAAAIKAIRESGMNLNPEVEGTLIRVPI.K.TREHREMLVKLAKQNTNK.KDSL.K
Retrocopy PQLILLNMASFPECTAAAIKAIRESGMNLNPEVEGTLIRVPILKATREHREMLVKLAKQNTNKTKDSLQK

Parental  VRTNAMNKL
          V..NAMNKL
Retrocopy VHINAMNKL

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Tupaia belangeri was not studied using RNA-Seq expression data.

ChIP-Seq

Tupaia belangeri was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_tbel_4411 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_4411 was not experimentally validated.

Homology

Retrocopy orthology:

Tupaia belangeri does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000007351	1 retrocopy	retro_cpor_877,
Homo sapiens	ENSG00000148187	1 retrocopy	retro_hsap_4897,
Gorilla gorilla	ENSGGOG00000023499	1 retrocopy	retro_ggor_98,
Mus musculus	ENSMUSG00000026887	1 retrocopy	retro_mmus_340,
Nomascus leucogenys	ENSNLEG00000017177	1 retrocopy	retro_nleu_1263,
Pongo abelii	ENSPPYG00000019570	1 retrocopy	retro_pabe_80,
Pan troglodytes	ENSPTRG00000021324	1 retrocopy	retro_ptro_3265,
Rattus norvegicus	ENSRNOG00000025997	2 retrocopies	retro_rnor_1477, retro_rnor_2654,
Sarcophilus harrisii	ENSSHAG00000012469	2 retrocopies	retro_shar_610, retro_shar_704,
Tupaia belangeri	ENSTBEG00000016569	1 retrocopy	retro_tbel_4411 ,