RetrogeneDB ID: retro_pabe_2810

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 5_random:9234189..9234780(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SMS
• Ensembl ID: ENSPPYG00000020182
• Aliases: None
• Description: spermine synthase [Source:HGNC Symbol;Acc:11123]

Sequence

>retro_pabe_2810
ATTCAGCAGAGTGATTTGACATATACCTGGGTCATCATGGGCAGCAGCAAAGTAGATTTCACTGGCAAAGAGGTACTGAT
TCTCAGAGGCTGAGATGGGGGCATATTATGTGAAATAGTCAAACTAAAATCAAAGATGGTCACTATGGTAGAGATTGACC
AAATGGTGATTGATGGATGTAAGAAATATATGCAAAAAACATGTGGTGATGTTGTAGACAATCTTAAAGGAGGCTGCTAT
CAAGCTCTGATAGAAGACTGCATTCCAATACTGAAGAGGTACACCAAAGAAGGGAGAGAATTGGATTGTGTGACTAACGA
TTTGACAGCTGTTCCAATCTCCACATCTCTGGAACAAGATTCCACGTGGGAGTTTCTCAGACTGATTTTTGACCCATGAA
TGGACATATTGAAACAGGATGGGAAATATTTTACACAGGGAAACTGTGTCAATCTGACAGAAGCCCTGCCACTCTATGAA
GAACAGCTTGGGTACCTGTATTGCCTTGTGGAATTCTCAAAGGAGATCGTCTATGTCCCTTCAAGCTTCAAATTGTGGGT
ATTTTACGCTGTCTGGAAGAAAGCTAAACCC

Alignment

ORF - retro_pabe_2810 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.22 %
• Parental protein coverage: 59.34 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LAESDLAYTRAIMGSGKEDYTGKDVLILGGGDGGILCEIVKLKPKMVTMVEIDQMVIDGCKKYMRKTCGD
          ...SDL.YT..IMGS.K.D.TGK.VLIL.G.DGGILCEIVKLK.KMVTMVEIDQMVIDGCKKYM.KTCGD
Retrocopy IQQSDLTYTWVIMGSSKVDFTGKEVLILRG*DGGILCEIVKLKSKMVTMVEIDQMVIDGCKKYMQKTCGD

Parental  VLDNLKGDCYQVLIEDCIPVLKRYAKEGREFDYVINDLTAVPISTSPEEDSTWEFLRLILDLSMKVLKQD
          V.DNLKG.CYQ.LIEDCIP.LKRY.KEGRE.D.V.NDLTAVPISTS.E.DSTWEFLRLI.D..M..LKQD
Retrocopy VVDNLKGGCYQALIEDCIPILKRYTKEGRELDCVTNDLTAVPISTSLEQDSTWEFLRLIFDP*MDILKQD

Parental  GKYFTQGNCVNLTEALSLYEEQLGRLYCPVEFSKEIVCVPSYLELWVFYTVWKKAKP
          GKYFTQGNCVNLTEAL.LYEEQLG.LYC.VEFSKEIV.VPS...LWVFY.VWKKAKP
Retrocopy GKYFTQGNCVNLTEALPLYEEQLGYLYCLVEFSKEIVYVPSSFKLWVFYAVWKKAKP

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_prefrontal_cortex	0.00 RPM	50.70 RPM
SRP007412_cerebellum	0.00 RPM	44.38 RPM
SRP007412_heart	0.00 RPM	28.06 RPM
SRP007412_kidney	0.00 RPM	31.06 RPM
SRP007412_liver	0.00 RPM	17.08 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2810 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2810 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2810 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 48 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000018382	1 retrocopy	retro_btau_1412,
Canis familiaris	ENSCAFG00000013284	3 retrocopies	retro_cfam_1076, retro_cfam_1995, retro_cfam_613,
Cavia porcellus	ENSCPOG00000006176	2 retrocopies	retro_cpor_729, retro_cpor_889,
Echinops telfairi	ENSETEG00000010098	2 retrocopies	retro_etel_1066, retro_etel_1540,
Homo sapiens	ENSG00000102172	5 retrocopies	retro_hsap_243, retro_hsap_3168, retro_hsap_3193, retro_hsap_3611, retro_hsap_4826,
Gorilla gorilla	ENSGGOG00000003123	3 retrocopies	retro_ggor_1335, retro_ggor_2437, retro_ggor_3009,
Microcebus murinus	ENSMICG00000000192	3 retrocopies	retro_mmur_1421, retro_mmur_1484, retro_mmur_699,
Myotis lucifugus	ENSMLUG00000013185	3 retrocopies	retro_mluc_471, retro_mluc_530, retro_mluc_92,
Macaca mulatta	ENSMMUG00000020392	2 retrocopies	retro_mmul_2003, retro_mmul_2574,
Monodelphis domestica	ENSMODG00000007897	1 retrocopy	retro_mdom_412,
Mus musculus	ENSMUSG00000071708	6 retrocopies	retro_mmus_2162, retro_mmus_2170, retro_mmus_2837, retro_mmus_3502, retro_mmus_3628, retro_mmus_994,
Nomascus leucogenys	ENSNLEG00000009955	4 retrocopies	retro_nleu_1664, retro_nleu_2200, retro_nleu_2208, retro_nleu_2755,
Oryctolagus cuniculus	ENSOCUG00000006016	2 retrocopies	retro_ocun_1458, retro_ocun_1918,
Pongo abelii	ENSPPYG00000020182	4 retrocopies	retro_pabe_2649, retro_pabe_2810 , retro_pabe_3752, retro_pabe_38,
Pteropus vampyrus	ENSPVAG00000016785	1 retrocopy	retro_pvam_524,
Rattus norvegicus	ENSRNOG00000007688	2 retrocopies	retro_rnor_1934, retro_rnor_938,
Tupaia belangeri	ENSTBEG00000012109	3 retrocopies	retro_tbel_1630, retro_tbel_1893, retro_tbel_3570,
Vicugna pacos	ENSVPAG00000007543	1 retrocopy	retro_vpac_50,