RetrogeneDB ID: retro_ogar_2407

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873620.1:560804..561385(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOGAG00000030857
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CD53
• Ensembl ID: ENSOGAG00000016713
• Aliases: None
• Description: CD53 molecule [Source:HGNC Symbol;Acc:1686]

Sequence

>retro_ogar_2407
ATGGGCATGAGTAGCTTGAAACTGCTGAAGTGTGTTCTGTCTTTCTTCAACTGCTCTTTTGGTACTGTGGCTGCTGCATT
TTGGGCTCTGGAATCTACTTCCTGGTCCACAACAACTTTGGAGTGCTCTTCCATGACTCCCCCTCCCTGGTAATCCATTC
GTCTTTGCCAGTGTGGGCCTGTTGCCATGGCGGCTGCATCCTGGGCTGCATGGGCTCTACCAGGGAGAACAAGTGCCTGC
TCATGTCAGTCTTCTTCATCCTGCTGCTGATAATCCTTCTTGCAGAGGTGATCTTGGCCATTCTGCTCTTTGTGTATGAA
AAGAAGCTGAAGGAGTACGTGGCTGAGGGCCTAACAAAGAGCATTCAGTGTTACCACTCGGACAATAGCACCAAGGAGGT
GTGGGACCCCATCCAGTCATTTCTACAGTGCTGTGGTGTAAATGGCACAAGTAATTGGTCCAGAGGCCCACCACTATCTT
GTCCCTCATATCCACAAGTGAAGGGCTGCTATACAAAAGCAAGACTGTGGTTTCAGTCCCATTTCCTACATATTGGAATC
ATCACCATCTCTGTATGTGTG

Alignment

ORF - retro_ogar_2407 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.39 %
• Parental protein coverage: 88.58 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MGMSSLKLLKYVLFFFN-LLFWFCGCCILGFGIYFLVHNNFGVLFHNLPSLTLGN-VFVIVG-SIIMVVA
          MGMSSLKLLK.VL.FFN.LLFW.CGCCILG.GIYFLVHNNFGVLFH..PSL.....VF..VG....M..A
Retrocopy MGMSSLKLLKCVLSFFN<LLFWYCGCCILGSGIYFLVHNNFGVLFHDSPSLVIHS<VFASVG<PVAMAAA

Parental  -FLGCMGSIKENKCLLMS-FFILLLIILLAEVTLAILLFVYEQKLSVYVAEDLTKSIDRYYSDNSTKVAW
          ..LGCMGS..ENKCLLMS.FFILLLIILLAEV.LAILLFVYE.KL..YVAE.LTKSI..Y.SDNSTK..W
Retrocopy <ILGCMGSTRENKCLLMSVFFILLLIILLAEVILAILLFVYEKKLKEYVAEGLTKSIQCYHSDNSTKEVW

Parental  DSIQSFLQCCGVNGTSDWSRGPPPSCPQDPQVKGCYTKARLWFQSNFLYIGIITICVCV
          D.IQSFLQCCGVNGTS.WSRGPP.SCP..PQVKGCYTKARLWFQS.FL.IGIITI.VCV
Retrocopy DPIQSFLQCCGVNGTSNWSRGPPLSCPSYPQVKGCYTKARLWFQSHFLHIGIITISVCV

Legend:

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

Expression

RNA-Seq

Otolemur garnettii was not studied using RNA-Seq expression data.

ChIP-Seq

Otolemur garnettii was not studied using ChIP-Seq data.

EST

Otolemur garnettii was not studied using EST data.

TSS

Otolemur garnettii was not studied using FANTOM5 data.

Lab

retro_ogar_2407 was not experimentally validated.

Homology

Retrocopy orthology:

Otolemur garnettii 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 9 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010760	2 retrocopies	retro_chof_116, retro_chof_307,
Homo sapiens	ENSG00000143119	1 retrocopy	retro_hsap_2960,
Gorilla gorilla	ENSGGOG00000005468	1 retrocopy	retro_ggor_2050,
Macaca mulatta	ENSMMUG00000000811	1 retrocopy	retro_mmul_1894,
Nomascus leucogenys	ENSNLEG00000003649	1 retrocopy	retro_nleu_1643,
Otolemur garnettii	ENSOGAG00000004869	1 retrocopy	retro_ogar_2827,
Otolemur garnettii	ENSOGAG00000008547	2 retrocopies	retro_ogar_1615, retro_ogar_3124,
Otolemur garnettii	ENSOGAG00000016713	2 retrocopies	retro_ogar_2407 , retro_ogar_469,
Pan troglodytes	ENSPTRG00000001085	1 retrocopy	retro_ptro_2004,