RetrogeneDB ID: retro_pabe_2316

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 3:79589493..79590235(-)
• Located in intron of: ENSPPYG00000013738

Retrocopy information

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

Parental gene information

• Parental gene symbol: DPPA4
• Ensembl ID: ENSPPYG00000013565
• Aliases: None
• Description: developmental pluripotency associated 4 [Source:HGNC Symbol;Acc:19200]

Sequence

>retro_pabe_2316
GAAGGGGACCAAATGCTCTGTCCAAAGAAGAAGGCAGAGTGCACTGACAACCCAGAACCTCAGAAGATGATACCAATCCC
TCCATTTCTTCTAATGTACCAGTGTCAATCAGATTCACTGGTACATTTTGTGGGCCTGGTGCCACCATTTAAAGCTGAGC
ACAGAGACCAGAAATTAGATGCACATAAGGGCCTGTGTTCTTTTGCCTACCCAAATCGAAAGGATATTCTTAGCTCAGGA
AAAAGAGGCCAGAATCTGGAAGATATTATGAAAAAAATCAAAGGTGGAAAAGGGGGAAATGTCCCTGCAAAGTTCTGAGG
AGATGCATCCTCCCAAAGTGGCTCTTCTTCCTGAGGAGGTGTTGCCTGCCCTGGTAGAGTCCGCTGCTCTCCTTGAAGGA
GTTAATACAGTTGTGGTGACAACTTCTGCCCTAGAGGCTTTGCTGGCCTCCTGGGCCAGAATTGCAGCCAGGGCAGGGAT
GCCAGAGGCAGTGAATGGAATCTCCACAAGAGTGGTGTCAAGTGGCGTGTGGTCCATGGGAGAAGTCTCCCTGCAGACAC
AGATGGTTGGGTTCACCTCCAGTTTCATGCTGGACAAGCCTGGGTTCCCGAGAAGCAGGAAGGGAGAGTGAGTGCACGCA
CGCCTCTTGCTTCCTGCCTCCAATTTTCCACTCCCACACCCTGCAGACAGTATGTTGAGCCCCAAATGTGTTCATAGGAA
CAAGATCTTCAGAAGCCTCCAG

Alignment

ORF - retro_pabe_2316 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.45 %
• Parental protein coverage: 81.52 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  KGNKVLCPKKKAEHTDNPRPQKKIPIPP-LPSKLP-PVNLIHRDILRAWCQQLKLSS-KGQKLDAYKRLC
          .G...LCPKKKAE.TDNP.PQK.IPIPP...S..P..VN.IH..IL.AWC..LKLS....QKLDA.K.LC
Retrocopy EGDQMLCPKKKAECTDNPEPQKMIPIPP<ISSNVP<SVNQIHWYILWAWCHHLKLST<RDQKLDAHKGLC

Parental  AFAYPNQKDFPSTAK-EAKIRKSLQKKLKVEKGETSLQSSQT-HPSEVALPPAGGPPALEDSTPLLEGVN
          .FAYPN.KD..S..K.EA.I.K.L.KK.KVEKGE.SLQSS...HP..VAL.P....PAL..S..LLEGVN
Retrocopy SFAYPNRKDILSSGK>EARIWKIL*KKSKVEKGEMSLQSSEEMHPPKVALLPEEVLPALVESAALLEGVN

Parental  TVVVTTSAPEALLASWARISARARTPEAV-ESPQEASGVRWCVVHGKSLPADTDGWVHLQFHAGQAWVPE
          TVVVTTSA.EALLASWARI.ARA..PEAV.E.....SGV.W.VVHG.SLPADTDGWVHLQFHAGQAWVPE
Retrocopy TVVVTTSALEALLASWARIAARAGMPEAV<EWNLHKSGVKWRVVHGRSLPADTDGWVHLQFHAGQAWVPE

Parental  K-QEGR-VSALFLLPASNFPPPHLEDNMLCPKCVHRNKVLIKSLQ
          K...G..V.A..LLPASNFP.PH..D.ML.PKCVHRNK....SLQ
Retrocopy K>RKGE*VHARLLLPASNFPLPHPADSMLSPKCVHRNKI-FRSLQ

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	0.11 RPM	0.00 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.03 RPM	0.00 RPM
SRP007412_kidney	0.10 RPM	0.00 RPM
SRP007412_liver	0.06 RPM	0.00 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2316 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2316 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2316 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Macaca mulatta	retro_mmul_1515

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 40 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000010335	5 retrocopies	retro_cfam_1332, retro_cfam_1540, retro_cfam_1905, retro_cfam_1934, retro_cfam_996,
Callithrix jacchus	ENSCJAG00000020171	2 retrocopies	retro_cjac_1334, retro_cjac_1491,
Echinops telfairi	ENSETEG00000002722	1 retrocopy	retro_etel_312,
Homo sapiens	ENSG00000121570	1 retrocopy	retro_hsap_893,
Gorilla gorilla	ENSGGOG00000015121	2 retrocopies	retro_ggor_1970, retro_ggor_723,
Loxodonta africana	ENSLAFG00000016804	1 retrocopy	retro_lafr_456,
Myotis lucifugus	ENSMLUG00000016423	1 retrocopy	retro_mluc_973,
Macaca mulatta	ENSMMUG00000016901	1 retrocopy	retro_mmul_1515,
Monodelphis domestica	ENSMODG00000018083	3 retrocopies	retro_mdom_1057, retro_mdom_1478, retro_mdom_999,
Mustela putorius furo	ENSMPUG00000010206	1 retrocopy	retro_mputfur_800,
Mus musculus	ENSMUSG00000058550	3 retrocopies	retro_mmus_1907, retro_mmus_2085, retro_mmus_3656,
Nomascus leucogenys	ENSNLEG00000004030	3 retrocopies	retro_nleu_2888, retro_nleu_3018, retro_nleu_388,
Oryctolagus cuniculus	ENSOCUG00000016435	1 retrocopy	retro_ocun_114,
Pongo abelii	ENSPPYG00000013565	3 retrocopies	retro_pabe_2316 , retro_pabe_2349, retro_pabe_770,
Pongo abelii	ENSPPYG00000013566	3 retrocopies	retro_pabe_1360, retro_pabe_2401, retro_pabe_346,
Pan troglodytes	ENSPTRG00000015200	2 retrocopies	retro_ptro_1923, retro_ptro_616,
Pteropus vampyrus	ENSPVAG00000010677	1 retrocopy	retro_pvam_1237,
Rattus norvegicus	ENSRNOG00000025404	4 retrocopies	retro_rnor_2750, retro_rnor_2996, retro_rnor_861, retro_rnor_862,
Sarcophilus harrisii	ENSSHAG00000017398	1 retrocopy	retro_shar_542,
Tursiops truncatus	ENSTTRG00000009508	1 retrocopy	retro_ttru_1772,