RetrogeneDB ID: retro_pabe_324

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:177585274..177585896(+)
• Located in intron of: ENSPPYG00000001352

Retrocopy information

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

Parental gene information

• Parental gene symbol: TRA2A
• Ensembl ID: ENSPPYG00000017728
• Aliases: None
• Description: transformer 2 alpha homolog (Drosophila) [Source:HGNC Symbol;Acc:16645]

Sequence

>retro_pabe_324
TCCAGATCCCGCTCTCACAGGAGACGAAGTAGCTCATATACACCAGAATACTTGCAGCGAAGGAGCCGAAGTCATTCTCC
AATGTCTAACCGGAGAAGACACACTGGCAGAAGGGCAAATCCAGATCCCAACACTTGCCTTAGAGTGTTTGGCCTTAGTT
TGTACACAACAGACAAAGATCTTCGTGAAGTATGTTCTCGATATGGACCTTTGAATGGTGCCAATGTAGTTTACAATCAG
CAAACTGGGCAATCTCAAGGATTTGCTTTTGTGTATTTTGAGGGAATAGATGACTCAAAGGAGGCTATGGTAAGGGCAAA
CAGAAAGGAGCTGGATGACAGAAGAAATTCGGGTGGATTATTCTATTACCAAGAGAATGCACACACCTACACCAGGCATC
TATATGGGCAGAACAACTCACAGTGGTGGTGGCAGAGGTGGTAGCAAAGGCGGCAGTGGAGGTGGTCACAGATGTCGAGA
TTCTTACTATGACAGAGGATATGATCATGGATATGACAGATATGAAAACTATGATTACCAGTACAGAAGACAATCACCTT
CTCCTTATTATAGTCGATACAGATCACAATCAAGATCTCATTCCTACAGCCCAAGACGCTAT

Alignment

ORF - retro_pabe_324 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.52 %
• Parental protein coverage: 74.47 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SHSHSHRRRSRSRSYTPEYRRRRSRSHSPMSNRRRHTGSRANPDPNTCLGVFGLSLYTTERDLREVFSRY
          S.S.SHRRRS.S..YTPEY..RRSRSHSPMSNRRRHTG.RANPDPNTCL.VFGLSLYTT..DLREV.SRY
Retrocopy SRSRSHRRRSSS--YTPEYLQRRSRSHSPMSNRRRHTGRRANPDPNTCLRVFGLSLYTTDKDLREVCSRY

Parental  GPLSGVNVVYDQRTGRSRGFAFVYFERIDDSKEAMERANGMELDGRR-IRVDYSITKRAHTPTPGIYMGR
          GPL.G.NVVY.Q.TG.S.GFAFVYFE.IDDSKEAM.RAN..ELD.RR.IRVDYSITKR.HTPTPGIYMGR
Retrocopy GPLNGANVVYNQQTGQSQGFAFVYFEGIDDSKEAMVRANRKELDDRR>IRVDYSITKRMHTPTPGIYMGR

Parental  PTHSGGGGGGGGGGGGGGGGRRRDSYYDRGYDRGYDRYEDYDYRYRRRSPSPYYSRYRSRSRSRSYSPRR
          .THS.GGG.GG..GG.GGG.R.RDSYYDRGYD.GYDRYE.YDY.YRR.SPSPYYSRYRS.SRS.SYSPRR
Retrocopy TTHS-GGGRGGSKGGSGGGHRCRDSYYDRGYDHGYDRYENYDYQYRRQSPSPYYSRYRSQSRSHSYSPRR

Parental  Y
          Y
Retrocopy Y

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	37.43 RPM
SRP007412_cerebellum	0.00 RPM	65.66 RPM
SRP007412_heart	0.00 RPM	23.24 RPM
SRP007412_kidney	0.00 RPM	34.11 RPM
SRP007412_liver	0.00 RPM	30.30 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_324 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_324 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_324 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001130	1 retrocopy	retro_chof_974,
Callithrix jacchus	ENSCJAG00000001509	1 retrocopy	retro_cjac_1759,
Echinops telfairi	ENSETEG00000007250	2 retrocopies	retro_etel_323, retro_etel_692,
Homo sapiens	ENSG00000164548	1 retrocopy	retro_hsap_386,
Gorilla gorilla	ENSGGOG00000009053	1 retrocopy	retro_ggor_391,
Mustela putorius furo	ENSMPUG00000013480	1 retrocopy	retro_mputfur_1442,
Nomascus leucogenys	ENSNLEG00000014794	1 retrocopy	retro_nleu_1481,
Otolemur garnettii	ENSOGAG00000009733	3 retrocopies	retro_ogar_1966, retro_ogar_2558, retro_ogar_3027,
Pongo abelii	ENSPPYG00000017728	1 retrocopy	retro_pabe_324 ,
Pongo abelii	ENSPPYG00000020314	1 retrocopy	retro_pabe_40,
Pongo abelii	ENSPPYG00000020771	3 retrocopies	retro_pabe_2548, retro_pabe_303, retro_pabe_766,
Pan troglodytes	ENSPTRG00000018988	1 retrocopy	retro_ptro_299,
Sorex araneus	ENSSARG00000012900	1 retrocopy	retro_sara_467,