RetrogeneDB ID: retro_hsap_410

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 1:78276548..78277466(-)
• Located in intron of: ENSG00000180488

Retrocopy information

• Ensembl ID: ENSG00000219201
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: AIDA
• Ensembl ID: ENSG00000186063
• Aliases: AIDA, C1orf80
• Description: axin interactor, dorsalization associated [Source:HGNC Symbol;Acc:25761]

Sequence

>retro_hsap_410
ATGTCGGAGGTGACCCGGAGTCTGCTGCAGCGCTGGGGCGCCAGTTTTAGGAGAGGCGCCGACTTCGACTCTTGGGGCCA
GCTGGTGGAGGCGATAGACGAGTATCAGATATTAGCAAGACATCTACAAAAGGAGGCCCAAGCTCAACACAATAATTCTG
AATTCACAGAAGAACAAAAGAAAACCATAGGCAAAATTGCAACATGCTTGGAATTGCGAAGTGCAGCTTTACAGTCCACA
CAGTCTCAAGAAGAATTTAAACTGGAGGACCTGAAGAAGCTAGAACCAATCCTAAAGAATATTCTTACATATAATAAAGA
ATTCCCATTTGATGTTCAGCCTGTCCCATTAAGAAGAATTTTGGCACCTGGTGAAGAAGAGAATTTGGAATTTGAAGAAG
ATGAAGAAGAGGGTGGTGCTGGAGCAGGGTCTCCTGATTCTTTTCCTGCTAGAGTTCCCGGTACTTTATTACCAAGGTTG
CCATCGGAACCAGGAATGACATTACTCACTATCAGAATTGCGAAAATTGGTTTGAAAGATGCTGGGCAGTGCATCGATCC
CTATATTACAGTTAGTGTAAAGGATCTGAATGGCATAGACTTAACTCCTGTGCAAGATACTCCTGTGGCTTCAAGAAAAG
AAGATACATATGTTCATTTTAATGTGGACATTGAGCTCCAGAAGCATGTTGAAAAATTAACCAAAGGTGCAGCTATCTTC
TTTGAATTCAAACCCTACAAGCCTAAAAAAAGGTTTACCAGCACCAAGTGTTTTGCTTTCATGGAGATGGATGAAATTAA
ACCTGGGCCAATTGTAATAGAACTATACAAGAAACCCACTGACTTTAAAAGAAAGAAATTGCAATTATTGACCAAGAAAC
CACTTTATCTTCATCTACATCAAACTTTGCACAAGGAA

Alignment

ORF - retro_hsap_410 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.35 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSEVTRSLLQRWGASFRRGADFDSWGQLVEAIDEYQILARHLQKEAQAQHNNSEFTEEQKKTIGKIATCL
          MSEVTRSLLQRWGASFRRGADFDSWGQLVEAIDEYQILARHLQKEAQAQHNNSEFTEEQKKTIGKIATCL
Retrocopy MSEVTRSLLQRWGASFRRGADFDSWGQLVEAIDEYQILARHLQKEAQAQHNNSEFTEEQKKTIGKIATCL

Parental  ELRSAALQSTQSQEEFKLEDLKKLEPILKNILTYNKEFPFDVQPVPLRRILAPGEEENLEFEEDEEEGGA
          ELRSAALQSTQSQEEFKLEDLKKLEPILKNILTYNKEFPFDVQPVPLRRILAPGEEENLEFEEDEEEGGA
Retrocopy ELRSAALQSTQSQEEFKLEDLKKLEPILKNILTYNKEFPFDVQPVPLRRILAPGEEENLEFEEDEEEGGA

Parental  GAGSPDSFPARVPGTLLPRLPSEPGMTLLTIRIEKIGLKDAGQCIDPYITVSVKDLNGIDLTPVQDTPVA
          GAGSPDSFPARVPGTLLPRLPSEPGMTLLTIRI.KIGLKDAGQCIDPYITVSVKDLNGIDLTPVQDTPVA
Retrocopy GAGSPDSFPARVPGTLLPRLPSEPGMTLLTIRIAKIGLKDAGQCIDPYITVSVKDLNGIDLTPVQDTPVA

Parental  SRKEDTYVHFNVDIELQKHVEKLTKGAAIFFEFKHYKPKKRFTSTKCFAFMEMDEIKPGPIVIELYKKPT
          SRKEDTYVHFNVDIELQKHVEKLTKGAAIFFEFK.YKPKKRFTSTKCFAFMEMDEIKPGPIVIELYKKPT
Retrocopy SRKEDTYVHFNVDIELQKHVEKLTKGAAIFFEFKPYKPKKRFTSTKCFAFMEMDEIKPGPIVIELYKKPT

Parental  DFKRKKLQLLTKKPLYLHLHQTLHKE
          DFKRKKLQLLTKKPLYLHLHQTLHKE
Retrocopy DFKRKKLQLLTKKPLYLHLHQTLHKE

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	0.62 RPM	61.03 RPM
bodymap2_adrenal	0.23 RPM	30.50 RPM
bodymap2_brain	0.38 RPM	23.46 RPM
bodymap2_breast	0.91 RPM	58.25 RPM
bodymap2_colon	0.62 RPM	81.60 RPM
bodymap2_heart	0.15 RPM	24.87 RPM
bodymap2_kidney	0.68 RPM	33.48 RPM
bodymap2_liver	0.00 RPM	13.94 RPM
bodymap2_lung	0.69 RPM	66.70 RPM
bodymap2_lymph_node	0.15 RPM	56.54 RPM
bodymap2_ovary	0.67 RPM	33.77 RPM
bodymap2_prostate	0.33 RPM	58.39 RPM
bodymap2_skeletal_muscle	0.24 RPM	16.48 RPM
bodymap2_testis	1.79 RPM	42.68 RPM
bodymap2_thyroid	0.36 RPM	29.17 RPM
bodymap2_white_blood_cells	0.18 RPM	36.70 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_410 was not detected

EST

No EST(s) were mapped for retro_hsap_410 retrocopy.

TSS

No TSS is located nearby retro_hsap_410 retrocopy 5' end.

Lab

retro_hsap_410 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_410 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 13 parental genes, and 31 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007593	2 retrocopies	retro_btau_1163, retro_btau_573,
Choloepus hoffmanni	ENSCHOG00000010095	2 retrocopies	retro_chof_1919, retro_chof_97,
Dasypus novemcinctus	ENSDNOG00000008380	5 retrocopies	retro_dnov_1765, retro_dnov_1909, retro_dnov_1961, retro_dnov_2172, retro_dnov_2280,
Homo sapiens	ENSG00000186063	4 retrocopies	retro_hsap_1901, retro_hsap_2076, retro_hsap_2998, retro_hsap_410 ,
Gorilla gorilla	ENSGGOG00000015289	3 retrocopies	retro_ggor_1394, retro_ggor_1627, retro_ggor_2077,
Macaca mulatta	ENSMMUG00000015025	1 retrocopy	retro_mmul_1918,
Monodelphis domestica	ENSMODG00000004774	3 retrocopies	retro_mdom_1417, retro_mdom_1418, retro_mdom_1448,
Nomascus leucogenys	ENSNLEG00000013583	1 retrocopy	retro_nleu_748,
Oryctolagus cuniculus	ENSOCUG00000017030	1 retrocopy	retro_ocun_688,
Pongo abelii	ENSPPYG00000000196	2 retrocopies	retro_pabe_2015, retro_pabe_2485,
Pan troglodytes	ENSPTRG00000002010	3 retrocopies	retro_ptro_1254, retro_ptro_1528, retro_ptro_2027,
Tarsius syrichta	ENSTSYG00000005745	3 retrocopies	retro_tsyr_101, retro_tsyr_1795, retro_tsyr_514,
Tursiops truncatus	ENSTTRG00000016594	1 retrocopy	retro_ttru_1084,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.09 RPM
CEU_NA11843	0.06 RPM
CEU_NA11930	0.16 RPM
CEU_NA12004	0.04 RPM
CEU_NA12400	0.00 RPM
CEU_NA12751	0.07 RPM
CEU_NA12760	0.22 RPM
CEU_NA12827	0.05 RPM
CEU_NA12872	0.08 RPM
CEU_NA12873	0.10 RPM
FIN_HG00183	0.14 RPM
FIN_HG00277	0.04 RPM
FIN_HG00315	0.08 RPM
FIN_HG00321	0.18 RPM
FIN_HG00328	0.07 RPM
FIN_HG00338	0.00 RPM
FIN_HG00349	0.11 RPM
FIN_HG00375	0.02 RPM
FIN_HG00377	0.03 RPM
FIN_HG00378	0.13 RPM
GBR_HG00099	0.12 RPM
GBR_HG00111	0.06 RPM
GBR_HG00114	0.00 RPM
GBR_HG00119	0.07 RPM
GBR_HG00131	0.09 RPM
GBR_HG00133	0.05 RPM
GBR_HG00134	0.20 RPM
GBR_HG00137	0.00 RPM
GBR_HG00142	0.08 RPM
GBR_HG00143	0.13 RPM
TSI_NA20512	0.00 RPM
TSI_NA20513	0.12 RPM
TSI_NA20518	0.25 RPM
TSI_NA20532	0.07 RPM
TSI_NA20538	0.09 RPM
TSI_NA20756	0.17 RPM
TSI_NA20765	0.04 RPM
TSI_NA20771	0.17 RPM
TSI_NA20786	0.05 RPM
TSI_NA20798	0.03 RPM
YRI_NA18870	0.78 RPM
YRI_NA18907	0.45 RPM
YRI_NA18916	0.06 RPM
YRI_NA19093	0.00 RPM
YRI_NA19099	0.32 RPM
YRI_NA19114	0.05 RPM
YRI_NA19118	0.50 RPM
YRI_NA19213	0.05 RPM
YRI_NA19214	0.74 RPM
YRI_NA19223	0.10 RPM

---

Indel association:

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