RetrogeneDB ID: retro_mdom_1554

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 5:242621160..242621833(-)
• Located in intron of: ENSMODG00000006509

Retrocopy information

• Ensembl ID: ENSMODG00000006504
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: FKBP3
• Ensembl ID: ENSMODG00000007352
• Aliases: None
• Description: FK506 binding protein 3, 25kDa [Source:HGNC Symbol;Acc:3719]

Sequence

>retro_mdom_1554
ATGGCGGCTGTAGGGCCACAGCGGACATGGAGTGCTGAGCAGCTGCTTAGCGAGGCACTCCCCAAGAAGGATATCATCAA
GTTTTTGCAGGACAACGGCTTGGATTCGTTTCTTGCAGAACATAAATTACTTGGAAACATAAAAAATGTGGCCAAGACAG
CAAACAAGAATCATTTAGTCACAGCCTACAACCACCTTTTTGAAAGTAAGTGTTTCAAAGGTACTGAGAGTGTTGCCAAA
TTGACAGAGCAAGTGAAAAGTGTGAAGCTTGATGAAGAGAAATCCAAAGAAAGTCAAACCTGAAGAGACTTTAGATGAGG
GGCCACCAAAATATACAAAATCTATTCTTAAGAAGGGAGATAAAACTAACTTTCCCAAAAAAGGAGATGTTGTTCATTGC
TGGTACACGGGAACTTTACAGGATGGAACTGTTTTTGATACTAATATTCAAACTAGTGCAAAGAAGAAAAAGAATGCTAA
GCCTCTAAGTTTTAAAGTTGGAGTGGGTAAAGTTATCAGAGGATGGGATGAAGCACTCTTAACAATGAGTAAAGGAGAAA
AGGCTCGCCTGGAGATTGAGCCTGAATGGGCTTATGGCAAGAAAGGACAGCCTGATGCAAAAATTCCACCAAATGCAAAA
CTCAATTTTGAAGTGGAATTAGTGGACATCGAT

Alignment

ORF - retro_mdom_1554 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.89 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAAAGPQRTWSAEQLRSEALPKKDIIKFLQDNGSDSFLAEHKLLGNIKNVAKTANKDHLVTAYNHLFESK
          MAA.GPQRTWSAEQL.SEALPKKDIIKFLQDNG.DSFLAEHKLLGNIKNVAKTANK.HLVTAYNHLFESK
Retrocopy MAAVGPQRTWSAEQLLSEALPKKDIIKFLQDNGLDSFLAEHKLLGNIKNVAKTANKNHLVTAYNHLFESK

Parental  RFKGTESVAKVTEQVKSVKLDEEKSKE-VKPEETLDEGPPKYTKSILKKGDKTNFPKKGDVVHCWYTGTL
          .FKGTESVAK.TEQVKSVKLDEEKSKE.VKPEETLDEGPPKYTKSILKKGDKTNFPKKGDVVHCWYTGTL
Retrocopy CFKGTESVAKLTEQVKSVKLDEEKSKE>VKPEETLDEGPPKYTKSILKKGDKTNFPKKGDVVHCWYTGTL

Parental  QDGTVFDTNIQTSAKKKKNAKPLSFKVGVGKVIRGWDEALLTMSKGEKARLEIEPEWAYGKKGQPDAKIP
          QDGTVFDTNIQTSAKKKKNAKPLSFKVGVGKVIRGWDEALLTMSKGEKARLEIEPEWAYGKKGQPDAKIP
Retrocopy QDGTVFDTNIQTSAKKKKNAKPLSFKVGVGKVIRGWDEALLTMSKGEKARLEIEPEWAYGKKGQPDAKIP

Parental  PNAKLNFEVELVDID
          PNAKLNFEVELVDID
Retrocopy PNAKLNFEVELVDID

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
SRP007412_brain	0.00 RPM	28.96 RPM
SRP007412_cerebellum	0.00 RPM	17.30 RPM
SRP007412_heart	0.00 RPM	46.65 RPM
SRP007412_kidney	0.00 RPM	23.70 RPM
SRP007412_liver	0.00 RPM	30.71 RPM
SRP007412_testis	0.00 RPM	27.50 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1554 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1554 was not experimentally validated.

Homology

Retrocopy orthology:

Monodelphis domestica 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 21 parental genes, and 52 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014018	4 retrocopies	retro_cfam_1788, retro_cfam_440, retro_cfam_616, retro_cfam_798,
Choloepus hoffmanni	ENSCHOG00000000189	1 retrocopy	retro_chof_2315,
Dipodomys ordii	ENSDORG00000009462	1 retrocopy	retro_dord_106,
Equus caballus	ENSECAG00000018299	2 retrocopies	retro_ecab_352, retro_ecab_565,
Echinops telfairi	ENSETEG00000003358	8 retrocopies	retro_etel_1114, retro_etel_1484, retro_etel_1491, retro_etel_1499, retro_etel_1774, retro_etel_2130, retro_etel_2200, retro_etel_997,
Felis catus	ENSFCAG00000027304	1 retrocopy	retro_fcat_1894,
Loxodonta africana	ENSLAFG00000003572	2 retrocopies	retro_lafr_357, retro_lafr_76,
Macropus eugenii	ENSMEUG00000004962	1 retrocopy	retro_meug_679,
Microcebus murinus	ENSMICG00000005808	2 retrocopies	retro_mmur_1582, retro_mmur_351,
Macaca mulatta	ENSMMUG00000016512	2 retrocopies	retro_mmul_2094, retro_mmul_735,
Monodelphis domestica	ENSMODG00000007352	1 retrocopy	retro_mdom_1554 ,
Monodelphis domestica	ENSMODG00000019554	2 retrocopies	retro_mdom_151, retro_mdom_733,
Mus musculus	ENSMUSG00000020949	1 retrocopy	retro_mmus_1322,
Otolemur garnettii	ENSOGAG00000003012	2 retrocopies	retro_ogar_2247, retro_ogar_3472,
Ochotona princeps	ENSOPRG00000011126	2 retrocopies	retro_opri_204, retro_opri_600,
Procavia capensis	ENSPCAG00000011316	2 retrocopies	retro_pcap_454, retro_pcap_78,
Rattus norvegicus	ENSRNOG00000004629	1 retrocopy	retro_rnor_1165,
Ictidomys tridecemlineatus	ENSSTOG00000002249	1 retrocopy	retro_itri_650,
Tupaia belangeri	ENSTBEG00000006017	13 retrocopies	retro_tbel_1032, retro_tbel_1125, retro_tbel_1696, retro_tbel_1783, retro_tbel_2151, retro_tbel_2569, retro_tbel_3297, retro_tbel_3567, retro_tbel_3807, retro_tbel_4222, retro_tbel_4482, retro_tbel_730, retro_tbel_800,
Tarsius syrichta	ENSTSYG00000002125	2 retrocopies	retro_tsyr_515, retro_tsyr_820,
Tursiops truncatus	ENSTTRG00000006664	1 retrocopy	retro_ttru_1041,