RetrogeneDB ID: retro_pabe_624

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 10:99102707..99103411(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TPM1
• Ensembl ID: ENSPPYG00000006534
• Aliases: None
• Description: tropomyosin 1 (alpha) [Source:HGNC Symbol;Acc:12010]

Sequence

>retro_pabe_624
GGCCCGCCGCAGGCGGTGAAACGCAAGATTCAGGCCCTGCCGCAGCAGGCGGACAAGGCGAAGACGGCGCGCAGGGCCTG
CAGCGGCAGCTGGACTGGAGGCCAGGTGGCTGTCCTCAACCGACGCATCCAGCTCGTTAAGGAGGAGTTGGACGGGGCTC
GGGAACGACTGGTCACGGCCCTGCAGAAGCTAGAGGAGGGGGAAAAGGCTGCAGATGAGCGTGAGAGAGAATGAAGGTGA
TAGAAAACCGGGTCATGAGGGATGAGGAGAAGATGGAGATTCAGGAGATGCAGCTCAAAGAGGTCAAGCGCACTGCGGCC
AGAGGCTGACCGCAAATACGAGGAGGTAGCTCGGAAGCTGACCGTCCTGGACGGCGAACTGGCCAGGGCAGAGGAGCGTG
CAGAGGTGTCTGAACTAAAATGTGGTGACCTGGCAGAAGAACTCAAGAATGTCACTAACAATCTGAAACCGCCGGAGGCT
GCACTGTAAAGTATTCTGAAAAGGAGGACAAATATGAAGAAAAAATTAAACTTCTGTCTGACAAACTGAAGGAGGCTGGG
ATCCTTGCTGAATTTGCGGAGATAATGGTTGCAAAACTGGAAAAGACAACTGATGACCTGGAAGAGAAATTTGCCCAGGC
CAAAGAAGAGAGTGTGGGCTTATATCAGACACTGGATCAGGCACTAAATGAACTTGATCGACTG

Alignment

ORF - retro_pabe_624 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.92 %
• Parental protein coverage: 71.47 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GTEDELDKYSEALKDAQEKLELAEKKATDA--EADVASLNRRIQLVEEELDRAQERLATALQKLEEAEKA
          G..........AL.....K...A............VA.LNRRIQLV.EELD.A.ERL.TALQKLEE.EKA
Retrocopy GPPQAVKRKIQALPQQADKAKTARRACSGSWTGGQVAVLNRRIQLVKEELDGARERLVTALQKLEEGEKA

Parental  ADESERG-MKVIESRAQKDEEKMEIQEIQLKEAKHIAE-DADRKYEEVARKLVIIESDLERAEERAELSE
          ADE.ER..MKVIE.R...DEEKMEIQE.QLKE.K..A...ADRKYEEVARKL......L.RAEERAE.SE
Retrocopy ADERERE<MKVIENRVMRDEEKMEIQEMQLKEVKRTAA>EADRKYEEVARKLTVLDGELARAEERAEVSE

Parental  GKCAELEEELKTVTNNLKSLEAQ-AEKYSQKEDKYEEEIKVLSDKLKEAETRAEFAERSVTKLEKSIDDL
          .KC..L.EELK.VTNNLK..EA....KYS.KEDKYEE.IK.LSDKLKEA...AEFAE..V.KLEK..DDL
Retrocopy LKCGDLAEELKNVTNNLKPPEAA<TVKYSEKEDKYEEKIKLLSDKLKEAGILAEFAEIMVAKLEKTTDDL

Parental  EEKVAHAKEENLSMHQMLDQTLLELNNM
          EEK.A.AKEE.....Q.LDQ.L.EL...
Retrocopy EEKFAQAKEESVGLYQTLDQALNELDRL

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	0.11 RPM	49.54 RPM
SRP007412_cerebellum	0.73 RPM	52.77 RPM
SRP007412_heart	0.06 RPM	2870.97 RPM
SRP007412_kidney	0.13 RPM	51.21 RPM
SRP007412_liver	0.09 RPM	56.25 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_624 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_624 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_624 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_609
Callithrix jacchus	retro_cjac_206

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000016966	1 retrocopy	retro_cfam_2167,
Choloepus hoffmanni	ENSCHOG00000012788	11 retrocopies	retro_chof_1194, retro_chof_1272, retro_chof_1360, retro_chof_1789, retro_chof_1829, retro_chof_2309, retro_chof_346, retro_chof_399, retro_chof_412, retro_chof_770, retro_chof_967,
Callithrix jacchus	ENSCJAG00000004355	2 retrocopies	retro_cjac_2200, retro_cjac_691,
Macropus eugenii	ENSMEUG00000014581	2 retrocopies	retro_meug_1944, retro_meug_2161,
Pongo abelii	ENSPPYG00000000787	2 retrocopies	retro_pabe_1230, retro_pabe_3263,
Pongo abelii	ENSPPYG00000006534	1 retrocopy	retro_pabe_624 ,
Ictidomys tridecemlineatus	ENSSTOG00000009955	1 retrocopy	retro_itri_166,
Tursiops truncatus	ENSTTRG00000003762	1 retrocopy	retro_ttru_446,
Vicugna pacos	ENSVPAG00000003277	1 retrocopy	retro_vpac_424,