RetrogeneDB ID: retro_hsap_4687

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: X:55987726..55988425(+)
• Located in intron of: ENSG00000227486

Retrocopy information

• Ensembl ID: ENSG00000214745
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: GOT2
• Ensembl ID: ENSG00000125166
• Aliases: GOT2, KAT4, KATIV, mitAAT
• Description: glutamic-oxaloacetic transaminase 2, mitochondrial [Source:HGNC Symbol;Acc:4433]

Sequence

>retro_hsap_4687
TCCTGGTGGACCTATGTGGAGATGGGACTTCCAGATCCCATCCTGGGAGTCACCAAAGCCTTTAAGAGGGACACCGATAG
CAAAAAGATGAATCTGGGAGTTTGTGTCTACTGGGATGATAATGGAAAGCCTTACATGCTGCTTAATGTCAACAAGGAAG
AGGCCCAGATTGCCACAAAAAATTTGGACAAAGAATACCTGCCCATTGGGGGTCTGGCTGAATTTTGCACGGCATCTGCA
GAACTAGCCCTGGGTGAGAATAGTGAAGTGTTGAAAAATGTCCAGTTATTCACTGTGCATACCATTTCTGGAACTGCGAC
CTTAACGATCAGAGCCTGTTTTCTGCAAAGATTTTTTAAGCTCAGCCAGGATGTCCAAACCATCCTGGGGAAATCACACA
CCCATCTTCAGGGATGCTGGCATGCAGCTACAAATTTATTGTTACTATGACCCCAAGACTTGGTGTTTGACTTCACAGGT
CGTATGGAGGACATTTCAAAAATACCAGAGCAAAGTGTTTTTCTGCATGCCTGTGCCCATAATCCCATGGGAGTGGAACC
TCGTCTAGAGCAGTGAAAAGAAATAGCAACAGTGGTGAAGAAAAATAATCTCTTTGCATTCTTTGACATGGCCTAGCAAG
GGTTTGCTAGTGATGATTGTAACAAGGATGCCTGGGCTGTGCACCACTTCATCAAAGAG

Alignment

ORF - retro_hsap_4687 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.9 %
• Parental protein coverage: 55.12 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SWWTHVEMGPPDPILGVTEAFKRDTNSKKMNLGVGAYRDDNGKPYVLPSVRKAEAQIAAKNLDKEYLPIG
          SWWT.VEMG.PDPILGVT.AFKRDT.SKKMNLGV..Y.DDNGKPY.L..V.K.EAQIA.KNLDKEYLPIG
Retrocopy SWWTYVEMGLPDPILGVTKAFKRDTDSKKMNLGVCVYWDDNGKPYMLLNVNKEEAQIATKNLDKEYLPIG

Parental  GLAEFCKASAELALGENSEVLKSGRFVTVQTISGTGALRIGAS-FLQRFFKFSRDVFLPKPTWGNHTPIF
          GLAEFC.ASAELALGENSEVLK.....TV.TISGT..L.I.A..F...F....R.....KP.WGNHTPIF
Retrocopy GLAEFCTASAELALGENSEVLKNVQLFTVHTISGTATLTIRAC>FCKDFLSSAR---MSKPSWGNHTPIF

Parental  RDAGMQLQGYRYYDPKT-CGFDFTGAVEDISKIPEQSVLLLHACAHNPTGVDPRPEQWKEIATVVKKRNL
          RDAGMQLQ.Y.YYDPKT...FDFTG..EDISKIPEQSV.L.HACAHNP.GV.PR.EQ.KEIATVVKK.NL
Retrocopy RDAGMQLQIYCYYDPKT<LVFDFTGRMEDISKIPEQSVFL-HACAHNPMGVEPRLEQ*KEIATVVKKNNL

Parental  FAFFDMAYQGFASGDGDKDAWAVRHFIEQ
          FAFFDMA.QGFAS.D..KDAWAV.HFI..
Retrocopy FAFFDMA*QGFASDDCNKDAWAVHHFIKE

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
bodymap2_adipose	0.00 RPM	45.34 RPM
bodymap2_adrenal	0.00 RPM	62.88 RPM
bodymap2_brain	0.12 RPM	124.49 RPM
bodymap2_breast	0.00 RPM	35.53 RPM
bodymap2_colon	0.00 RPM	59.05 RPM
bodymap2_heart	0.00 RPM	441.02 RPM
bodymap2_kidney	0.00 RPM	146.98 RPM
bodymap2_liver	0.00 RPM	199.66 RPM
bodymap2_lung	0.00 RPM	44.67 RPM
bodymap2_lymph_node	0.00 RPM	56.81 RPM
bodymap2_ovary	0.02 RPM	75.12 RPM
bodymap2_prostate	0.00 RPM	108.48 RPM
bodymap2_skeletal_muscle	0.00 RPM	198.41 RPM
bodymap2_testis	0.00 RPM	70.04 RPM
bodymap2_thyroid	0.06 RPM	113.35 RPM
bodymap2_white_blood_cells	0.00 RPM	47.55 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_4687 was not detected

EST

No EST(s) were mapped for retro_hsap_4687 retrocopy.

TSS

No TSS is located nearby retro_hsap_4687 retrocopy 5' end.

Lab

retro_hsap_4687 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_4687 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_2912

---

Parental genes homology:

Parental genes homology involve 11 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017346	3 retrocopies	retro_amel_1805, retro_amel_815, retro_amel_846,
Canis familiaris	ENSCAFG00000008357	2 retrocopies	retro_cfam_586, retro_cfam_816,
Callithrix jacchus	ENSCJAG00000011234	1 retrocopy	retro_cjac_2916,
Homo sapiens	ENSG00000125166	4 retrocopies	retro_hsap_4687 , retro_hsap_473, retro_hsap_960, retro_hsap_971,
Gorilla gorilla	ENSGGOG00000005767	3 retrocopies	retro_ggor_2912, retro_ggor_449, retro_ggor_774,
Microcebus murinus	ENSMICG00000008954	1 retrocopy	retro_mmur_480,
Macaca mulatta	ENSMMUG00000006000	1 retrocopy	retro_mmul_1337,
Mustela putorius furo	ENSMPUG00000004862	1 retrocopy	retro_mputfur_567,
Pongo abelii	ENSPPYG00000007413	3 retrocopies	retro_pabe_3640, retro_pabe_823, retro_pabe_901,
Pan troglodytes	ENSPTRG00000008185	4 retrocopies	retro_ptro_3115, retro_ptro_354, retro_ptro_665, retro_ptro_670,
Rattus norvegicus	ENSRNOG00000011782	1 retrocopy	retro_rnor_2695,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.02 RPM
CEU_NA11843	0.00 RPM
CEU_NA11930	0.07 RPM
CEU_NA12004	0.00 RPM
CEU_NA12400	0.00 RPM
CEU_NA12751	0.00 RPM
CEU_NA12760	0.00 RPM
CEU_NA12827	0.05 RPM
CEU_NA12872	0.03 RPM
CEU_NA12873	0.00 RPM
FIN_HG00183	0.00 RPM
FIN_HG00277	0.04 RPM
FIN_HG00315	0.00 RPM
FIN_HG00321	0.03 RPM
FIN_HG00328	0.05 RPM
FIN_HG00338	0.02 RPM
FIN_HG00349	0.00 RPM
FIN_HG00375	0.00 RPM
FIN_HG00377	0.03 RPM
FIN_HG00378	0.00 RPM
GBR_HG00099	0.03 RPM
GBR_HG00111	0.02 RPM
GBR_HG00114	0.00 RPM
GBR_HG00119	0.00 RPM
GBR_HG00131	0.03 RPM
GBR_HG00133	0.00 RPM
GBR_HG00134	0.00 RPM
GBR_HG00137	0.03 RPM
GBR_HG00142	0.03 RPM
GBR_HG00143	0.03 RPM
TSI_NA20512	0.00 RPM
TSI_NA20513	0.02 RPM
TSI_NA20518	0.00 RPM
TSI_NA20532	0.07 RPM
TSI_NA20538	0.00 RPM
TSI_NA20756	0.00 RPM
TSI_NA20765	0.06 RPM
TSI_NA20771	0.03 RPM
TSI_NA20786	0.00 RPM
TSI_NA20798	0.06 RPM
YRI_NA18870	0.03 RPM
YRI_NA18907	0.03 RPM
YRI_NA18916	0.00 RPM
YRI_NA19093	0.03 RPM
YRI_NA19099	0.00 RPM
YRI_NA19114	0.05 RPM
YRI_NA19118	0.00 RPM
YRI_NA19213	0.00 RPM
YRI_NA19214	0.02 RPM
YRI_NA19223	0.04 RPM

---

Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).