RetrogeneDB ID: retro_pabe_3438

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 9:94371512..94372257(+)
• Located in intron of: ENSPPYG00000019435

Retrocopy information

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

Parental gene information

• Parental gene symbol: DKFZP459O0215
• Ensembl ID: ENSPPYG00000017639
• Aliases: None
• Description: Septin-7 [Source:UniProtKB/Swiss-Prot;Acc:Q5R481]

Sequence

>retro_pabe_3438
AGTATCATCTCACTTATTGCCACAGCAGACACACTCACACCAGAGGAATGCTAACAGTTTAAAAAACAGATAATGAAAGA
AATCCAAGAACATAAAATTAAAATATATGAATTTCTAGAAACAGACAATAAAGAAGAAAATAAACTTGTTTAAAAGATAA
AGGACCATTTACTTGTTGGTGTGGTAGGTAGTAATACTATCATTGAAGTTAATGGCAAAATGATCAGAGGAAAGCAGTAT
CCTTGGGGTACTGCTGAAGTTGAAAATGGTGAACATTGTGATTTTACAATTCTAAGAAATATGTTGATAAGAACACCCAT
GCAGGACTTGAAAGATGTTACTAATAATATCCACTATGAGAACTACAGAAGCAGAAAACTGGCAGCTGTGACTTATAATG
GAATTGATAACAACAAGAATAAAGGGCAGCTGACCAAGAGCCCTCTGGCACAAATGGAAGAAGAAAGAAGGGAGCATGTA
GCTAAAATGAAGAAGATGGAGCTGGAGATGGAGCAGGTGTTTGAGATGAAGGTCAAAGAAAAAGTTCAAAACTGAAGAAC
TCTGAAGCTGAGCTCCAGCGGCACCATGAGCAAATGAAAACGAATTTGGAAGCACAGCATAAACAATCAGAGGAAAAAAG
TCATCAGAGGATGAGAAAGCAAACTGGGAAGCTCAACAACGTATTTTAGAACAACAGAACTCTTTGAGAACCTTGGAAAA
GAACAAGAAGAAAGGAAGAGCTTTT

Alignment

ORF - retro_pabe_3438 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.75 %
• Parental protein coverage: 65.1 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NIIPLIAKADTLTPEECQQFKKQIMKEIQEHKIKIYEFPETDDEEENKLVKKIKDRLPLAVVGSNTIIEV
          .II.LIA.ADTLTPEEC.QFKKQIMKEIQEHKIKIYEF.ETD..EENKLV.KIKD.L...VVGSNTIIEV
Retrocopy SIISLIATADTLTPEEC*QFKKQIMKEIQEHKIKIYEFLETDNKEENKLV*KIKDHLLVGVVGSNTIIEV

Parental  NGKRVRGRQYPWGVAEVENGEHCDFTILRNMLIRTHMQDLKDVTNNVHYENYRSRKLAAVTYNGVDNNKN
          NGK..RG.QYPWG.AEVENGEHCDFTILRNMLIRT.MQDLKDVTNN.HYENYRSRKLAAVTYNG.DNNKN
Retrocopy NGKMIRGKQYPWGTAEVENGEHCDFTILRNMLIRTPMQDLKDVTNNIHYENYRSRKLAAVTYNGIDNNKN

Parental  KGQLTKSPLAQMEEERREHVAKMKKMEMEMEQVFEMKVKEKVQ-KLKDSEAELQRRHEQMKKNLEAQHKE
          KGQLTKSPLAQMEEERREHVAKMKKME.EMEQVFEMKVKEKVQ.KLK.SEAELQR.H....K........
Retrocopy KGQLTKSPLAQMEEERREHVAKMKKMELEMEQVFEMKVKEKVQ<KLKNSEAELQR-HHEQMKTNLEAQHK

Parental  LEEKR-RQFEDEKANWEAQQRILEQQNSSRTLEKNKKKGKIF
          ..E......EDEKANWEAQQRILEQQNS.RTLEKNKKKG..F
Retrocopy QSEEK<KSSEDEKANWEAQQRILEQQNSLRTLEKNKKKGRAF

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	160.56 RPM
SRP007412_cerebellum	0.00 RPM	129.75 RPM
SRP007412_heart	0.00 RPM	67.13 RPM
SRP007412_kidney	0.00 RPM	36.93 RPM
SRP007412_liver	0.00 RPM	32.50 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3438 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3438 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3438 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4202
Pan troglodytes	retro_ptro_2853
Gorilla gorilla	retro_ggor_2816

---

Parental genes homology:

Parental genes homology involve 15 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012276	2 retrocopies	retro_cjac_1259, retro_cjac_3809,
Equus caballus	ENSECAG00000022693	1 retrocopy	retro_ecab_650,
Echinops telfairi	ENSETEG00000015624	3 retrocopies	retro_etel_1263, retro_etel_282, retro_etel_517,
Homo sapiens	ENSG00000122545	2 retrocopies	retro_hsap_3810, retro_hsap_4202,
Gorilla gorilla	ENSGGOG00000001175	1 retrocopy	retro_ggor_2816,
Monodelphis domestica	ENSMODG00000021167	1 retrocopy	retro_mdom_1672,
Nomascus leucogenys	ENSNLEG00000001673	1 retrocopy	retro_nleu_2152,
Otolemur garnettii	ENSOGAG00000006015	1 retrocopy	retro_ogar_1193,
Pongo abelii	ENSPPYG00000012144	1 retrocopy	retro_pabe_3335,
Pongo abelii	ENSPPYG00000017639	1 retrocopy	retro_pabe_3438 ,
Pan troglodytes	ENSPTRG00000019080	2 retrocopies	retro_ptro_2585, retro_ptro_2853,
Rattus norvegicus	ENSRNOG00000006545	9 retrocopies	retro_rnor_1424, retro_rnor_1425, retro_rnor_1426, retro_rnor_1427, retro_rnor_1428, retro_rnor_1431, retro_rnor_1445, retro_rnor_1446, retro_rnor_821,
Sarcophilus harrisii	ENSSHAG00000003788	1 retrocopy	retro_shar_258,
Ictidomys tridecemlineatus	ENSSTOG00000021378	3 retrocopies	retro_itri_1332, retro_itri_1736, retro_itri_1771,
Tursiops truncatus	ENSTTRG00000016197	1 retrocopy	retro_ttru_329,