RetrogeneDB ID: retro_hsap_2216

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 2:224569343..224570008(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000226539
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MLX
• Ensembl ID: ENSG00000108788
• Aliases: MLX, MAD7, MXD7, TCFL4, bHLHd13
• Description: MLX, MAX dimerization protein [Source:HGNC Symbol;Acc:11645]

Sequence

>retro_hsap_2216
GAGCCAGGTGCCTCTCCCAAAGACCCCTGGGTAAAGGTGGAGTACATCTACAGCTACAAAAGCTCAGACCTCACGTATTT
TATAGAAAGCACCCACAATGGGACAGTAGTGTCTAGAGCTAATAGCATCGGTTCCACCAGTGCCTCTTCCATCCCCAACA
CAGATGAGGAGGACAGTGATTACCACCAAGAGTCCTACAAGGACCAGTAGTGGTGAGCACACACTGAGGCTGAGCAGAAG
AGGAAGGATGTCATCAAGAGAGGCTGTGATGACCTTCAGACCATCATCCCCACATGCCAGCAGCAGGACTCCTGCATTGG
CTCCCGAAAGCTCAGCAAAGCCATCGTTCTACAAAAGACCATTGACTACACTCAGTTTTTGCACAAGGAGAAGAAAATGC
AGGAGGAGGAGGTGTCCACACTATGCAAGGACCTCACAGCCCTAAAGATCATGAAAGGGAACTATAAGCAGATTGTGAAG
GCACACCAGGACAACCCCCATGAGGGGAGGACCAGGCCTCTGACCAAGTCAAGGTCAGTGTGTTTCGAGGTATCACGAAC
TCCCTGTTCCAGTCCTTCAATGTCTTCATCTCTGTGACCAACTTCTAGGAGCTGTCAGCCTGTGTCTTCAGATAGATTGA
GGAGCACTGCAAGCCACAGGCCATG

Alignment

ORF - retro_hsap_2216 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.09 %
• Parental protein coverage: 92.62 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EPGASPEDPWVKVEYAYSDNSLDPGLFVESTRKGSVVSRANSIGSTSASSVPNTDDEDSDYHQEAYKESY
          EPGASP.DPWVKVEY.YS..S.D...F.EST..G.VVSRANSIGSTSASS.PNTD.EDSDYHQ....ESY
Retrocopy EPGASPKDPWVKVEYIYSYKSSDLTYFIESTHNGTVVSRANSIGSTSASSIPNTDEEDSDYHQ----ESY

Parental  KDRRRRAHTQAEQKRRDAIKRGYDDLQTIVPTCQQQDFSIGSQKLSKAIVLQKTIDYIQFLHKEKKKQEE
          KD....AHT.AEQKR.D.IKRG.DDLQTI.PTCQQQD..IGS.KLSKAIVLQKTIDY.QFLHKEKK.QEE
Retrocopy KDQ*W*AHTEAEQKRKDVIKRGCDDLQTIIPTCQQQDSCIGSRKLSKAIVLQKTIDYTQFLHKEKKMQEE

Parental  EVSTLRKDVTALKIMKVNYEQIVKAHQDNPHE-GEDQVSDQVKFNVFQGIMDSLFQSFNASISVASFQEL
          EVSTL.KD.TALKIMK.NY.QIVKAHQDNPHE.GEDQ.SDQVK..VF.GI..SLFQSFN..ISV..F.EL
Retrocopy EVSTLCKDLTALKIMKGNYKQIVKAHQDNPHE<GEDQASDQVKVSVFRGITNSLFQSFNVFISVTNF*EL

Parental  SACVFSWIEEHCKPQTL
          SACVF..IEEHCKPQ..
Retrocopy SACVFR*IEEHCKPQAM

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	27.45 RPM
bodymap2_adrenal	0.04 RPM	30.72 RPM
bodymap2_brain	0.00 RPM	8.51 RPM
bodymap2_breast	0.00 RPM	30.04 RPM
bodymap2_colon	0.00 RPM	22.72 RPM
bodymap2_heart	0.04 RPM	43.40 RPM
bodymap2_kidney	0.04 RPM	37.99 RPM
bodymap2_liver	0.00 RPM	36.23 RPM
bodymap2_lung	0.00 RPM	23.49 RPM
bodymap2_lymph_node	0.00 RPM	43.16 RPM
bodymap2_ovary	0.08 RPM	17.64 RPM
bodymap2_prostate	0.02 RPM	39.18 RPM
bodymap2_skeletal_muscle	0.00 RPM	84.32 RPM
bodymap2_testis	0.04 RPM	17.23 RPM
bodymap2_thyroid	0.06 RPM	34.86 RPM
bodymap2_white_blood_cells	0.00 RPM	54.46 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_2216 was not detected

EST

No EST(s) were mapped for retro_hsap_2216 retrocopy.

TSS

No TSS is located nearby retro_hsap_2216 retrocopy 5' end.

Lab

retro_hsap_2216 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_2216 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1681
Gorilla gorilla	retro_ggor_1748
Pongo abelii	retro_pabe_2087

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005011	1 retrocopy	retro_cjac_2774,
Homo sapiens	ENSG00000108788	1 retrocopy	retro_hsap_2216 ,
Gorilla gorilla	ENSGGOG00000010869	1 retrocopy	retro_ggor_1748,
Microcebus murinus	ENSMICG00000010258	1 retrocopy	retro_mmur_1373,
Monodelphis domestica	ENSMODG00000014918	2 retrocopies	retro_mdom_501, retro_mdom_539,
Nomascus leucogenys	ENSNLEG00000011638	1 retrocopy	retro_nleu_2338,
Pongo abelii	ENSPPYG00000008387	1 retrocopy	retro_pabe_2087,
Pan troglodytes	ENSPTRG00000009208	1 retrocopy	retro_ptro_1681,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.02 RPM
CEU_NA11843	0.06 RPM
CEU_NA11930	0.00 RPM
CEU_NA12004	0.00 RPM
CEU_NA12400	0.14 RPM
CEU_NA12751	0.05 RPM
CEU_NA12760	0.09 RPM
CEU_NA12827	0.05 RPM
CEU_NA12872	0.03 RPM
CEU_NA12873	0.10 RPM
FIN_HG00183	0.16 RPM
FIN_HG00277	0.15 RPM
FIN_HG00315	0.14 RPM
FIN_HG00321	0.18 RPM
FIN_HG00328	0.05 RPM
FIN_HG00338	0.06 RPM
FIN_HG00349	0.00 RPM
FIN_HG00375	0.12 RPM
FIN_HG00377	0.05 RPM
FIN_HG00378	0.00 RPM
GBR_HG00099	0.00 RPM
GBR_HG00111	0.09 RPM
GBR_HG00114	0.03 RPM
GBR_HG00119	0.14 RPM
GBR_HG00131	0.03 RPM
GBR_HG00133	0.12 RPM
GBR_HG00134	0.15 RPM
GBR_HG00137	0.11 RPM
GBR_HG00142	0.08 RPM
GBR_HG00143	0.03 RPM
TSI_NA20512	0.06 RPM
TSI_NA20513	0.00 RPM
TSI_NA20518	0.11 RPM
TSI_NA20532	0.07 RPM
TSI_NA20538	0.14 RPM
TSI_NA20756	0.09 RPM
TSI_NA20765	0.08 RPM
TSI_NA20771	0.11 RPM
TSI_NA20786	0.00 RPM
TSI_NA20798	0.06 RPM
YRI_NA18870	0.03 RPM
YRI_NA18907	0.03 RPM
YRI_NA18916	0.06 RPM
YRI_NA19093	0.08 RPM
YRI_NA19099	0.05 RPM
YRI_NA19114	0.16 RPM
YRI_NA19118	0.02 RPM
YRI_NA19213	0.14 RPM
YRI_NA19214	0.02 RPM
YRI_NA19223	0.04 RPM

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Indel association:

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