RetrogeneDB ID: retro_hsap_2460

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 20:21723091..21723715(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000233015
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SLC25A6
• Ensembl ID: ENSG00000169100
• Aliases: None
• Description: solute carrier family 25 (mitochondrial carrier; adenine nucleotide translocator), member 6 [Source:HGNC Symbol;Acc:10992]

Sequence

>retro_hsap_2460
TCCCAAATGGCCGTGGCTCAGATCCAGCAGGTCAAGCTGCTGCTGCTGCAGGGGCAACATGCCAGTAGCAGATTGCAGCC
CACAAGCAGCACGAAGTGTGGTGGATGGACTGCGTCCTCTGCATCTCCAAGGAGCATGGGGCTGTCTTCCTGGAAGGGCA
ACCTTGCCAGTGCCATCCATTACTTCCCATGCAAGCCCTTAACTTTGCCTTCAAGGATAAGTACAAGCAGTTCTTCCTGG
GGGTGCAGACAAGCGCATGCAGTTCTGGAGGTGCTTCGCTGGCCACCCGGCCTTGGGTGGCCTGGCTGGCACCACCTCAC
TCTGCTTCATGTACCCCCTGGATTTCCCAGAACCTCCTGGCAGCAGACATTGGGAAATTGGGCACAGTGCATGAGTTCAA
AGACCTGGGAGCCTGGCCGGTGAGGATCACCAAATCCAATGGACCCAGGGCCTGTACCAGGGCTTCAGCATCTCATGCAA
GACATCATCATCTACCCAGCAGCCTCCTTCTGCTAGTAGGATACAGCTGAGGGCATGCTCCCCAGCCCCAAGAACATGCA
CATCCTGGCAAGCTGAGTTACTGCAAAGACTATGAGGGCCATGGCCAACATGATCTCCTATCCT

Alignment

ORF - retro_hsap_2460 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.36 %
• Parental protein coverage: 70.13 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 8

Retrocopy - Parental Gene Alignment:

Parental  SKTAVAPIERVKLLL-QVQHASK-QIAADKQYK-GIVDCIVRIPKEQGVLSFWRG-NLANVIRYF-PTQA
          S..AVA.I..VKLLL.Q.QHAS..QIAA.KQ......DC...I.KE.G...F..G.NLA..I.YF.P.QA
Retrocopy SQMAVAQIQQVKLLLLQGQHASS<QIAAHKQHEVWWMDCVLCISKEHGAV-FLEG>NLASAIHYF<PMQA

Parental  LNFAFKDKYKQIFL-GGVDKHTQFWRYFAGNLASGGAAGATSLCFVYPLD-FARTRLAADVG-KSGTERE
          LNFAFKDKYKQ.FL.GG.DK..QFWR.FAG..A.GG.AG.TSLCF.YPLD.F.RT......G.K.GT..E
Retrocopy LNFAFKDKYKQFFL<GGADKRMQFWRCFAGHPALGGLAGTTSLCFMYPLD<FPRTSWQQTLG<KLGTVHE

Parental  FRGLGDCLVKITKSDGIR-GLYQGFSVS-VQGIIIYRAAYFGVYDTAKGMLPDPKNTHIVVSWMIAQTVT
          F..LG...V.ITKS.G.R.GLYQGFS.S..Q.IIIY.AA.F...DTA.GMLP.PKN.HI..S...A.T..
Retrocopy FKDLGAWPVRITKSNGPR<GLYQGFSIS<MQDIIIYPAASFC**DTAEGMLPSPKNMHILAS*VTAKTMR

Parental  AVAGVVSYP
          A.A...SYP
Retrocopy AMANMISYP

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	314.07 RPM
bodymap2_adrenal	0.00 RPM	338.52 RPM
bodymap2_brain	0.00 RPM	77.31 RPM
bodymap2_breast	0.00 RPM	243.60 RPM
bodymap2_colon	0.00 RPM	328.05 RPM
bodymap2_heart	0.00 RPM	54.59 RPM
bodymap2_kidney	0.00 RPM	175.14 RPM
bodymap2_liver	0.00 RPM	42.12 RPM
bodymap2_lung	0.00 RPM	179.15 RPM
bodymap2_lymph_node	0.00 RPM	193.70 RPM
bodymap2_ovary	0.00 RPM	334.67 RPM
bodymap2_prostate	0.00 RPM	261.14 RPM
bodymap2_skeletal_muscle	0.00 RPM	72.51 RPM
bodymap2_testis	0.02 RPM	138.91 RPM
bodymap2_thyroid	0.00 RPM	240.40 RPM
bodymap2_white_blood_cells	0.00 RPM	294.37 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_2460 was not detected

EST

No EST(s) were mapped for retro_hsap_2460 retrocopy.

TSS

No TSS is located nearby retro_hsap_2460 retrocopy 5' end.

Lab

retro_hsap_2460 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_2460 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005609	1 retrocopy	retro_amel_255,
Homo sapiens	ENSG00000005022	7 retrocopies	retro_hsap_2243, retro_hsap_3132, retro_hsap_3336, retro_hsap_3516, retro_hsap_3715, retro_hsap_3730, retro_hsap_4239,
Homo sapiens	ENSG00000169100	5 retrocopies	retro_hsap_1207, retro_hsap_150, retro_hsap_2460 , retro_hsap_4147, retro_hsap_4207,
Gorilla gorilla	ENSGGOG00000023004	2 retrocopies	retro_ggor_239, retro_ggor_2785,
Loxodonta africana	ENSLAFG00000001584	1 retrocopy	retro_lafr_713,
Microcebus murinus	ENSMICG00000006136	2 retrocopies	retro_mmur_1021, retro_mmur_922,
Macaca mulatta	ENSMMUG00000006899	1 retrocopy	retro_mmul_1182,
Nomascus leucogenys	ENSNLEG00000000389	1 retrocopy	retro_nleu_895,
Otolemur garnettii	ENSOGAG00000000963	2 retrocopies	retro_ogar_2492, retro_ogar_2499,

Population studies

Expression level across human populations :

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

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Indel association:

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