RetrogeneDB ID: retro_pabe_225

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:21997979..21998551(+)
• Located in intron of: ENSPPYG00000000155

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM133B
• Ensembl ID: ENSPPYG00000025825
• Aliases: None
• Description: family with sequence similarity 133, member B [Source:HGNC Symbol;Acc:28629]

Sequence

>retro_pabe_225
GCCTATATGAACCTAATAGCAATGGCAAGATCAAGGGGTCCAATCCAGTCTTCAGGGCCAACAATACAGGATTATTTGAA
TCAACCAAGTCCTACCTGGGAAGAAGTAAAAGAGCAACTAGAAGAGGAGAAAAGAAAGGCTCCAAGGCTTTGGCTGAATT
TGAAGAAAAAATGAATGAGAACTGGAAGAAAGAACTAGAAAAACACAGGGAGAAATTGTTAAGTGGAAGTGAGAGCTCAT
CAAAAAAAAAAAAAGAAAAGAATAAATCTGGTAGGTATTCATCTTCTTCTTCAACAAGCTCTAATTCTTCCAGCAGTTCT
TCTGATTGTGAAGATGAGGATAAGAAACAAGGAAAACAGAGAAAGAAAAAGAACCGTTCACATAAATCTTCTGAAAGCTC
CATGTCATAAACTGAATCAGACAGTAAGGATAGTTTAAAAAAGAAAAAGACATCAAAAGATGCAACTGAGAAAGAAAAGG
ACATTAAAGGACTCAGCAAAAAGAGAACGACAAATTCTTAAGATAAAACTTTATCATCCGAGTCCTTGTCAGAATCACAG
TATATTGGGGAG

Alignment

ORF - retro_pabe_225 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.79 %
• Parental protein coverage: 86.6 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AYMNPIAMARSRGPIQSSGPTIQDYLNRPR---EEVKEQL-EKK-KKGSKALAEFEEKMNENWKKELEKH
          AYMN.IAMARSRGPIQSSGPTIQDYLN.P....EEVKEQL.E.K.KKGSKALAEFEEKMNENWKKELEKH
Retrocopy AYMNLIAMARSRGPIQSSGPTIQDYLNQPSPTWEEVKEQLEEEK<KKGSKALAEFEEKMNENWKKELEKH

Parental  REKLLSGSESS----SKKRQYSSSSSSSSDSSSSSS---DSEDEDKKQGKRRKKKKNRSHKSSESSMSET
          REKLLSGSESS......K......SSSSS.SS.SSS...D.EDEDKKQGK.R.KKKNRSHKSSESSMS.T
Retrocopy REKLLSGSESSXXXXXEKNKSGRYSSSSSTSSNSSSSSSDCEDEDKKQGKQR-KKKNRSHKSSESSMS*T

Parental  ESDSKDSLKKKKKSKDGTEKEKDIKGLSKKRKMYSEDKPLSSESLSESEYIEE
          ESDSKDSLKKKK.SKD.TEKEKDIKGLSKKR...S.DK.LSSESLSES.YI.E
Retrocopy ESDSKDSLKKKKTSKDATEKEKDIKGLSKKRTTNS*DKTLSSESLSESQYIGE

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	1.71 RPM
SRP007412_cerebellum	0.00 RPM	2.43 RPM
SRP007412_heart	0.00 RPM	1.02 RPM
SRP007412_kidney	0.00 RPM	1.69 RPM
SRP007412_liver	0.00 RPM	1.25 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_225 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_225 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_225 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Macaca mulatta	retro_mmul_420

---

Parental genes homology:

Parental genes homology involve 14 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007438	1 retrocopy	retro_amel_102,
Callithrix jacchus	ENSCJAG00000013910	3 retrocopies	retro_cjac_1084, retro_cjac_1163, retro_cjac_4095,
Equus caballus	ENSECAG00000026810	1 retrocopy	retro_ecab_95,
Homo sapiens	ENSG00000234545	4 retrocopies	retro_hsap_2336, retro_hsap_3179, retro_hsap_55, retro_hsap_577,
Loxodonta africana	ENSLAFG00000029755	1 retrocopy	retro_lafr_594,
Myotis lucifugus	ENSMLUG00000005933	1 retrocopy	retro_mluc_2301,
Macaca mulatta	ENSMMUG00000019802	4 retrocopies	retro_mmul_1415, retro_mmul_226, retro_mmul_420, retro_mmul_765,
Mus musculus	ENSMUSG00000058503	2 retrocopies	retro_mmus_3481, retro_mmus_3519,
Nomascus leucogenys	ENSNLEG00000015333	1 retrocopy	retro_nleu_14,
Pongo abelii	ENSPPYG00000025825	1 retrocopy	retro_pabe_225 ,
Rattus norvegicus	ENSRNOG00000009163	1 retrocopy	retro_rnor_2891,
Sus scrofa	ENSSSCG00000015317	1 retrocopy	retro_sscr_49,
Ictidomys tridecemlineatus	ENSSTOG00000028195	1 retrocopy	retro_itri_12,
Tupaia belangeri	ENSTBEG00000011674	1 retrocopy	retro_tbel_1,