RetrogeneDB ID: retro_pabe_2068

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2b:77086277..77086810(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MED28
• Ensembl ID: ENSPPYG00000014627
• Aliases: None
• Description: mediator complex subunit 28 [Source:HGNC Symbol;Acc:24628]

Sequence

>retro_pabe_2068
ATGGCAGCTCCACCAGGTGTTATGTTCCCTAGGGAGCCACTGGGTCCCCCACCACCCTAGCTTGGAACTCCCAAGCTAGG
CTTTGCTTCTTCAGGAAGCTCCAGGTTCTCTGAGACCTTATGACAGTACCTTGATGGAAAAGTTGAAGTCATATTTTCAG
GCTTGCTTTGCTTCTCTGGTGAGTCAGAACTGTGTCAATGGCACCAATCAGGAAGAAATTCAAACTGGTGTTGATCAGTA
TATCCAAGAGTTTCTGGATATTGCAAGACAGATAGGATGTTTTTTTCTTCAAAAAGATTGCAATGATCTGTCCAGAAACC
AGATAATGCTATCAAAGAGGATTTCTTAGAACTAAGGAATGAATTATAGTGGAAAGACATGCTGGTCCAGAAGAACTTGA
TATAGTTGCGGCATTCACAGCAGGTGCTGGAGGACATCAATGTGCAGCACAAAAAGCTAGCCGACATCCCTCAGGGTTCC
CTGGCCTATCTTGAGTAGGCATCTGCCAATATATTGCACCTCTGAAGCCAACC

Alignment

ORF - retro_pabe_2068 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.82 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAAPLGGMFSGQPPGPPQAPPG-LPGQASLLQAAPGAPRPSSSTLVDELESSFEACFASLVSQDYVNGTD
          MAAP.G.MF...P.GPP....G.LP..A.LLQ.APG..RP..STL...L.S.F.ACFASLVSQ..VNGT.
Retrocopy MAAPPGVMFPREPLGPPPP*LG>LPS*ALLLQEAPGSLRPYDSTLMEKLKSYFQACFASLVSQNCVNGTN

Parental  QEEIRTGVDQCIQKFLDIARQTECFFLQK-RLQLSVQKPEQVIKEDVSELRNELQRKDALVQKHLTKLRH
          QEEI.TGVDQ.IQ.FLDIARQ..CFFLQK.RLQ.SVQKP...IKED..ELRNEL..KD.LVQK.L..LRH
Retrocopy QEEIQTGVDQYIQEFLDIARQIGCFFLQK<RLQ*SVQKPDNAIKEDFLELRNEL*WKDMLVQKNLI*LRH

Parental  WQQVLEDINVQHKKPADIPQGSLAYLEQASANI-PAPLKPT
          .QQVLEDINVQHKK.ADIPQGSLAYLE.ASANI..APLKPT
Retrocopy SQQVLEDINVQHKKLADIPQGSLAYLE*ASANI<IAPLKPT

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	8.74 RPM
SRP007412_cerebellum	0.00 RPM	8.51 RPM
SRP007412_heart	0.00 RPM	7.71 RPM
SRP007412_kidney	0.00 RPM	7.16 RPM
SRP007412_liver	0.00 RPM	6.85 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2068 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2068 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2068 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2188
Pan troglodytes	retro_ptro_1666
Gorilla gorilla	retro_ggor_1733
Macaca mulatta	retro_mmul_916
Callithrix jacchus	retro_cjac_2746

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Parental genes homology:

Parental genes homology involve 22 parental genes, and 67 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001760	1 retrocopy	retro_amel_1649,
Bos taurus	ENSBTAG00000019441	1 retrocopy	retro_btau_973,
Callithrix jacchus	ENSCJAG00000012711	8 retrocopies	retro_cjac_1545, retro_cjac_1708, retro_cjac_2117, retro_cjac_2603, retro_cjac_2746, retro_cjac_3016, retro_cjac_4156, retro_cjac_848,
Cavia porcellus	ENSCPOG00000012616	2 retrocopies	retro_cpor_1165, retro_cpor_207,
Dasypus novemcinctus	ENSDNOG00000008526	2 retrocopies	retro_dnov_2276, retro_dnov_2595,
Dipodomys ordii	ENSDORG00000008042	1 retrocopy	retro_dord_116,
Homo sapiens	ENSG00000118579	5 retrocopies	retro_hsap_2188, retro_hsap_2465, retro_hsap_2860, retro_hsap_589, retro_hsap_919,
Gorilla gorilla	ENSGGOG00000001114	5 retrocopies	retro_ggor_1534, retro_ggor_1733, retro_ggor_1978, retro_ggor_409, retro_ggor_519,
Loxodonta africana	ENSLAFG00000016936	1 retrocopy	retro_lafr_693,
Microcebus murinus	ENSMICG00000006792	2 retrocopies	retro_mmur_1172, retro_mmur_545,
Myotis lucifugus	ENSMLUG00000001351	1 retrocopy	retro_mluc_1997,
Macaca mulatta	ENSMMUG00000005734	5 retrocopies	retro_mmul_1468, retro_mmul_2453, retro_mmul_507, retro_mmul_639, retro_mmul_916,
Monodelphis domestica	ENSMODG00000000813	1 retrocopy	retro_mdom_1175,
Nomascus leucogenys	ENSNLEG00000016620	3 retrocopies	retro_nleu_2816, retro_nleu_284, retro_nleu_317,
Oryctolagus cuniculus	ENSOCUG00000001576	4 retrocopies	retro_ocun_1473, retro_ocun_1474, retro_ocun_337, retro_ocun_444,
Otolemur garnettii	ENSOGAG00000033835	4 retrocopies	retro_ogar_2031, retro_ogar_3387, retro_ogar_493, retro_ogar_998,
Ochotona princeps	ENSOPRG00000003932	2 retrocopies	retro_opri_134, retro_opri_382,
Pongo abelii	ENSPPYG00000014627	4 retrocopies	retro_pabe_1811, retro_pabe_2068 , retro_pabe_2363, retro_pabe_601,
Pan troglodytes	ENSPTRG00000015939	3 retrocopies	retro_ptro_1424, retro_ptro_1666, retro_ptro_431,
Pteropus vampyrus	ENSPVAG00000015716	1 retrocopy	retro_pvam_641,
Ictidomys tridecemlineatus	ENSSTOG00000000930	10 retrocopies	retro_itri_1064, retro_itri_1201, retro_itri_1437, retro_itri_1622, retro_itri_1660, retro_itri_1671, retro_itri_176, retro_itri_236, retro_itri_462, retro_itri_770,
Tursiops truncatus	ENSTTRG00000006177	1 retrocopy	retro_ttru_484,