RetrogeneDB ID: retro_tbel_4545

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_89643:11838..12177(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: COX7A2L
• Ensembl ID: ENSTBEG00000014124
• Aliases: None
• Description: cytochrome c oxidase subunit VIIa polypeptide 2 like [Source:HGNC Symbol;Acc:2289]

Sequence

>retro_tbel_4545
CTGTACTACAAGTTTAGTGGTTTCATGGAGAAGTTGGCGGGATCATGGGCTTCAGATGCCTATAGTCCACAGGGATTAAA
GCCTGTGGCTTCTGCAGACCCACCACCTATCATATTTGCCACACCAACTAAATTGACCTCTAATTCCACTGTATAAGATT
ATACTGGGAAAAACAAAGTTCCAGAGCTACAGATTTTCCAGAAATCTGATGGTGTGCCCACTCACTTGAAACGAGGTCTT
CCTGACCAAATGCTTTACCAGACCACCATGGCACTGACTGTAGGAGGGACCATCTACTGTCTGATCACAATCTACATAGC
TTCAAAGCCCAGAAATAAA

Alignment

ORF - retro_tbel_4545 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.84 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MYYKFSGFTQKLAGAWASDAYSPQGLKPVASAEAPPIIFATPTKLTSNSTVYDYNGKNKVPELQKIFQKS
          .YYKFSGF..KLAG.WASDAYSPQGLKPVASA..PPIIFATPTKLTSNSTV.DY.GKNKVPELQ.IFQKS
Retrocopy LYYKFSGFMEKLAGSWASDAYSPQGLKPVASADPPPIIFATPTKLTSNSTV*DYTGKNKVPELQ-IFQKS

Parental  DGVPIHLKRGLPDQMLYRTTMALTVGGTIYCLIALYMASQPRNK
          DGVP.HLKRGLPDQMLY.TTMALTVGGTIYCLI..Y.AS.PRNK
Retrocopy DGVPTHLKRGLPDQMLYQTTMALTVGGTIYCLITIYIASKPRNK

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_4545 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_4545 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 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000032040	1 retrocopy	retro_cfam_1847,
Macaca mulatta	ENSMMUG00000016278	1 retrocopy	retro_mmul_110,
Mustela putorius furo	ENSMPUG00000008875	1 retrocopy	retro_mputfur_97,
Mus musculus	ENSMUSG00000024248	2 retrocopies	retro_mmus_32, retro_mmus_926,
Oryctolagus cuniculus	ENSOCUG00000027189	3 retrocopies	retro_ocun_1617, retro_ocun_1781, retro_ocun_28,
Otolemur garnettii	ENSOGAG00000016029	1 retrocopy	retro_ogar_114,
Sarcophilus harrisii	ENSSHAG00000012014	1 retrocopy	retro_shar_479,
Ictidomys tridecemlineatus	ENSSTOG00000012922	1 retrocopy	retro_itri_21,
Tupaia belangeri	ENSTBEG00000007294	7 retrocopies	retro_tbel_1177, retro_tbel_178, retro_tbel_3617, retro_tbel_4102, retro_tbel_4330, retro_tbel_738, retro_tbel_781,
Tupaia belangeri	ENSTBEG00000014124	3 retrocopies	retro_tbel_2384, retro_tbel_4472, retro_tbel_4545 ,