RetrogeneDB ID: retro_pabe_391

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:57554362..57554704(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ITGB1BP1
• Ensembl ID: ENSPPYG00000012667
• Aliases: ITGB1BP1, DKFZP459I196
• Description: Integrin beta-1-binding protein 1 [Source:UniProtKB/Swiss-Prot;Acc:Q5R5S7]

Sequence

>retro_pabe_391
CACAGTAGTAGCAGTTCCCAAAGTGGTGAAATCAGTACTAAGAGCAAGTCTGTAGATTCCAGCCTTGGGGGCCTTTCATA
GCCCAGCCCTGTGGCCAGCCTCAATACAGATTCCACCAAGAGTGCAGAATAAAGCAACAATAATTCAAATACGTGTGCAG
AACTTCAAATAAAATATGTTGGTGCCATTAAGACACTGAAACTCTCTGAGAGAAGATGTCTTGAAGGGCCACTAGACCTG
ATAAATTATATAGATGTTGCCCAGCAAGATGAAAAGTTGCCTCTTGTTCCTCTGGAGGAAAAATTTATAATGGGAGTTTC
CAAATATAATACAAGTATCAAC

Alignment

ORF - retro_pabe_391 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.19 %
• Parental protein coverage: 57. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  HSSSSSQSSEISTKSKSVDSSLGGLSRSSTVASLDTDSTKSSGQSNSNSDTCAEFRIKYVGAIEKLKLSE
          HSSSSSQS.EISTKSKSVDSSLGGLS..S.VASL.TDSTKS...SN.NS.TCAE..IKYVGAI..LKLSE
Retrocopy HSSSSSQSGEISTKSKSVDSSLGGLS*PSPVASLNTDSTKSAE*SNNNSNTCAELQIKYVGAIKTLKLSE

Parental  GKDLEGPLDLINYIDVAQQDGKLPFVPPEEEFIMGVSKYGIKVS
          ...LEGPLDLINYIDVAQQD.KLP.VP.EE.FIMGVSKY.....
Retrocopy RRCLEGPLDLINYIDVAQQDEKLPLVPLEEKFIMGVSKYNTSIN

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	54.35 RPM
SRP007412_cerebellum	0.00 RPM	49.25 RPM
SRP007412_heart	0.03 RPM	34.83 RPM
SRP007412_kidney	0.00 RPM	23.27 RPM
SRP007412_liver	0.00 RPM	12.15 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_391 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_391 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_391 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_277
Pan troglodytes	retro_ptro_231
Gorilla gorilla	retro_ggor_321
Macaca mulatta	retro_mmul_563

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 35 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000013063	2 retrocopies	retro_btau_1221, retro_btau_1435,
Choloepus hoffmanni	ENSCHOG00000013602	2 retrocopies	retro_chof_1385, retro_chof_432,
Callithrix jacchus	ENSCJAG00000006250	3 retrocopies	retro_cjac_1650, retro_cjac_2776, retro_cjac_393,
Dasypus novemcinctus	ENSDNOG00000008930	3 retrocopies	retro_dnov_1422, retro_dnov_2198, retro_dnov_727,
Homo sapiens	ENSG00000119185	1 retrocopy	retro_hsap_277,
Gorilla gorilla	ENSGGOG00000001754	1 retrocopy	retro_ggor_321,
Macropus eugenii	ENSMEUG00000006761	1 retrocopy	retro_meug_1434,
Microcebus murinus	ENSMICG00000002359	7 retrocopies	retro_mmur_1251, retro_mmur_1342, retro_mmur_1375, retro_mmur_1523, retro_mmur_1539, retro_mmur_244, retro_mmur_442,
Myotis lucifugus	ENSMLUG00000010629	2 retrocopies	retro_mluc_1218, retro_mluc_1752,
Macaca mulatta	ENSMMUG00000018036	1 retrocopy	retro_mmul_563,
Nomascus leucogenys	ENSNLEG00000013322	1 retrocopy	retro_nleu_1488,
Oryctolagus cuniculus	ENSOCUG00000003726	1 retrocopy	retro_ocun_120,
Otolemur garnettii	ENSOGAG00000001679	4 retrocopies	retro_ogar_1235, retro_ogar_1383, retro_ogar_2353, retro_ogar_981,
Procavia capensis	ENSPCAG00000005976	1 retrocopy	retro_pcap_241,
Pongo abelii	ENSPPYG00000012667	1 retrocopy	retro_pabe_391 ,
Pan troglodytes	ENSPTRG00000011637	1 retrocopy	retro_ptro_231,
Sorex araneus	ENSSARG00000009799	1 retrocopy	retro_sara_735,
Tarsius syrichta	ENSTSYG00000014537	1 retrocopy	retro_tsyr_225,
Tursiops truncatus	ENSTTRG00000000859	1 retrocopy	retro_ttru_712,