RetrogeneDB ID: retro_pabe_2015

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2a:101363145..101364063(-)
• Located in intron of: ENSPPYG00000012647

Retrocopy information

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

Parental gene information

• Parental gene symbol: AIDA
• Ensembl ID: ENSPPYG00000000196
• Aliases: None
• Description: Axin interactor, dorsalization-associated protein [Source:UniProtKB/Swiss-Prot;Acc:Q5RAV3]

Sequence

>retro_pabe_2015
ATGTCAGAGGTGACCCGGAGTCTGCTGCAGCGCTGGGGTGCCAGTTTTAGGAGAGGCGCTGACTGCGACTCTTGGGGCCA
GCTGGTGGAGGCGATAGACGAGTATCAGATATTAGCAAGACATCTCCAAAAAGAGGCCCAAGCTCAACACAATAATTTTG
AATTCACAGAAGAACAAAAGAAAACCATAGGCAAAATTGCAACATGCTTAGAATTGCGAAGTGCAGCTTTACAGTCCACA
CAGCCTCAAGAAGAATTTAAACCGGAGAACCTGAAGAAGCTAGAACCAATCCTAAAGAATATTCTTACATATAATAAAGA
ATTCCCATTTGATGTTTAGCCTGTCCTGTTAAGAAGAATTTTGGCACCTGGTGAAGAAGAGAATTTGGAATTTGAAGAAG
ATGAAGAAGAGGGTGATGCTGGAGCAGGGTCTCCTGATTCTTTTCCTGCTAGAGTTCCCGGTACTTTCTTATCAAGGTTG
CCATCGGAACCAGGAATGACATTACTCACTATCAGAATTGAGAAAATTGGTTTGAAAGATGCTGGGCAGTGCATCGATCC
CCATATTACAGTTAATGTAAAGGATCTGAATGGCATAGACTTAACTCCTGTGCAAGATACTCCTGTGGCTTCAAGAAAAG
AAGATATATATGTTCATTTTAATGTGGACATTGAGCTCCAGAAGCATGTTGAAAAATTAACCAAAGGTGCAGCTATCTTC
TTTGAATTCAAACACTACAAGCCTAAAAAAAGGTTTACCAGCACCAAGTGTTTTGCTTTCATGGAGATGGATGAAATTAA
ACCTGGGCCAATTGTAATAGAACTATACAAGAAGCCCACTGACTTGAAAAGAAAGCAATTGCAATTACTGACCAAGAAAC
CACTTTATCTTCATCTACATCAAACTTTGCACAAGGAA

Alignment

ORF - retro_pabe_2015 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.1 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSEVTRSLLQRWGASFRRGADFDSWGQLVEAIDEYQILARHLQKEAQAQHNNSEFTEEQKKTIGKIATCL
          MSEVTRSLLQRWGASFRRGAD.DSWGQLVEAIDEYQILARHLQKEAQAQHNN.EFTEEQKKTIGKIATCL
Retrocopy MSEVTRSLLQRWGASFRRGADCDSWGQLVEAIDEYQILARHLQKEAQAQHNNFEFTEEQKKTIGKIATCL

Parental  ELRSAALQSTQSQEEFKLEDLKKLEPILKNILTYNKEFPFDVQPVPLRRILAPGEEENLEFEEDEEEGGA
          ELRSAALQSTQ.QEEFK.E.LKKLEPILKNILTYNKEFPFDV.PV.LRRILAPGEEENLEFEEDEEEG.A
Retrocopy ELRSAALQSTQPQEEFKPENLKKLEPILKNILTYNKEFPFDV*PVLLRRILAPGEEENLEFEEDEEEGDA

Parental  GAGSPDSFPARVPGTLLPRLPSEPGMTLLTIRIEKIGLKDAGQCIDPYITVSVKDLNGIDLTPVQDTPVA
          GAGSPDSFPARVPGT.L.RLPSEPGMTLLTIRIEKIGLKDAGQCIDP.ITV.VKDLNGIDLTPVQDTPVA
Retrocopy GAGSPDSFPARVPGTFLSRLPSEPGMTLLTIRIEKIGLKDAGQCIDPHITVNVKDLNGIDLTPVQDTPVA

Parental  SRKEDTYVHFNVDIELQKHVEKLTKGAAIFFEFKHYKPKKRFTSTKCFAFMEMDEIKPGPIVIELYKKPT
          SRKED.YVHFNVDIELQKHVEKLTKGAAIFFEFKHYKPKKRFTSTKCFAFMEMDEIKPGPIVIELYKKPT
Retrocopy SRKEDIYVHFNVDIELQKHVEKLTKGAAIFFEFKHYKPKKRFTSTKCFAFMEMDEIKPGPIVIELYKKPT

Parental  DFKRKKLQLLTKKPLYLHLHQTLHKE
          D.KRK.LQLLTKKPLYLHLHQTLHKE
Retrocopy DLKRKQLQLLTKKPLYLHLHQTLHKE

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	8.68 RPM
SRP007412_cerebellum	0.12 RPM	9.36 RPM
SRP007412_heart	0.06 RPM	7.22 RPM
SRP007412_kidney	0.00 RPM	7.13 RPM
SRP007412_liver	0.00 RPM	4.50 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2015 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2015 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2015 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2076
Pan troglodytes	retro_ptro_1528
Gorilla gorilla	retro_ggor_1627

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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,