RetrogeneDB ID: retro_ptro_1666

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 2B:190970640..190971164(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MED28
• Ensembl ID: ENSPTRG00000015939
• Aliases: None
• Description: mediator complex subunit 28 [Source:HGNC Symbol;Acc:24628]

Sequence

>retro_ptro_1666
CCACCAGGTGTTATGTTCCCTGTGGAGCCACTGGGTCCCCCACCACCCCCACTGGAACTCCCAAGCTAGGCTTTGCTTCT
TCAGGAAGCTCCAGGTTCTCTAAGACCTTATGACAGTACCTTGATGGAAAAGTTGAAGTCATATTTTCAGACTTGCTTTG
CTTCTCTGGTGAGTCAGAAGTATGTCAATGGCACCAATCAGGAAGAAATTCAAACTGGTGTTGATCAGTGTATCCAGGAG
TTTCTGGATATTGCAAGACAGATAGGATGTTTTTTTCTTCAAAAAGATTGCAATTATCTGTCCAGAAACCAGATAATGCT
ATCAAAGAGGATTTCTTCGAACTAAGGAATGAATTATAGTGGAAAGACATGCTGGTCCAGAAGAACTTGACATAGTTGCG
GCATTCACGGCAGGTGCTGGAGGACATCAATGTGCAGCACAGAAAGCTAGCCGACATCCCTCAGGGTTCCTTGGCCTATC
TTGAGTAGGCATCTGCCAATATACTTGCACCTCTGAAGCCAACC

Alignment

ORF - retro_ptro_1666 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.73 %
• Parental protein coverage: 97.77 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PLGGMFSGQPPGPPQAPPGLPGQASLLQAAPGAPRPSSSTLVDELESSFEACFASLVSQDYVNGTDQEEI
          P.G.MF...P.GPP..P..LP..A.LLQ.APG..RP..STL...L.S.F..CFASLVSQ.YVNGT.QEEI
Retrocopy PPGVMFPVEPLGPPPPPLELPS*ALLLQEAPGSLRPYDSTLMEKLKSYFQTCFASLVSQKYVNGTNQEEI

Parental  RTGVDQCIQKFLDIARQTECFFLQ-KRLQLSVQKPEQVIKEDVSELRNELQRKDALVQKHLTKLRHWQQV
          .TGVDQCIQ.FLDIARQ..CFFLQ.KRLQLSVQKP...IKED..ELRNEL..KD.LVQK.LT.LRH..QV
Retrocopy QTGVDQCIQEFLDIARQIGCFFLQ<KRLQLSVQKPDNAIKEDFFELRNEL*WKDMLVQKNLT*LRHSRQV

Parental  LEDINVQHKKPADIPQGSLAYLEQASANIPAPLKPT
          LEDINVQH.K.ADIPQGSLAYLE.ASANI.APLKPT
Retrocopy LEDINVQHRKLADIPQGSLAYLE*ASANILAPLKPT

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	5.99 RPM
SRP007412_cerebellum	0.07 RPM	7.24 RPM
SRP007412_heart	0.06 RPM	5.22 RPM
SRP007412_kidney	0.10 RPM	6.69 RPM
SRP007412_liver	0.07 RPM	3.83 RPM
SRP007412_testis	0.11 RPM	4.53 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1666 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1666 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1666 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2188
Gorilla gorilla	retro_ggor_1733
Pongo abelii	retro_pabe_2068
Macaca mulatta	retro_mmul_916
Callithrix jacchus	retro_cjac_2746

---

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,