RetrogeneDB ID: retro_pabe_1963

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2a:72929189..72929922(+)
• Located in intron of: ENSPPYG00000012478

Retrocopy information

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

Parental gene information

• Parental gene symbol: ASS1
• Ensembl ID: ENSPPYG00000019692
• Aliases: None
• Description: argininosuccinate synthase [Source:RefSeq peptide;Acc:NP_001126812]

Sequence

>retro_pabe_1963
TCATCTGGCCTGTATGAGGACTGCTACCTCCGGGGCCCCTCTCTTCCCAGGCCTTACGTCACCCACAAACAAGTGGAAAT
TGCTCAGTGGGAGGAGGCAAAGTATGTGTCCCACAGTGCCATGGGAAAGAGGAACGATCAGGTCTGGTTTGAGCTCGCCT
GCTACTCGCTGGCCCCCCAGATTAAGGTCATTGCTCCCGGGAGGATCCCCGAGTTCTACAACCAGTTCAAGGGCCGCAGT
GATCTGATGGAATACGCAGAGAAACATGGGATTCCCATTGCAGTCACGCTGAAGCACCCATGGAACATGGACGAGAACCT
CATGCACATCAGCCATGAGGCTGGAATCTTGGAGAACCCCAAGAAACAAGCACCTTCAGGTCTCTACATGAAGATCCAGG
ACCCAGCCAAAGCCCCCAACACCCCCGACATTTTCAAGATTGAGTGAAAAAGGGGTCCCTGTGAAGGTGACCAGCATCAA
GGATGGCACCACCCACCAGACCTCCTTGGAGCTTTTCATGTACCTGAATGAAGTCGCAGGCAAGCACAGCGTGGGCCATA
TTGACATCGTGGAGAACCGCTTCATTGAAATGAAGTCCTGAGGTATCTGCAAGACCCCAGCAGGCACCATCCTTTACCAC
TCTCATTTAGACATTGAGGCCTTCACCATGGAACAGGAAGTGCACAAAATCAAACAAGGCCTGGGCTTGAAATTTGCTGA
GTTGGTGTACACC

Alignment

ORF - retro_pabe_1963 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.57 %
• Parental protein coverage: 68.25 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SSALYEDRYLLGTSLARPCIARKQVEIAQQEGAKYVSHGATGKGNDQVRFELSCYSLAPQIKVIAPWRMP
          SS.LYED.YL.G.SL.RP....KQVEIAQ.E.AKYVSH.A.GK.NDQV.FEL.CYSLAPQIKVIAP.R.P
Retrocopy SSGLYEDCYLRGPSLPRPYVTHKQVEIAQWEEAKYVSHSAMGKRNDQVWFELACYSLAPQIKVIAPGRIP

Parental  EFYNRFKGRNDLMEYAKQHGIPIPVTPKNPWSMDENLMHISYEAGILENPKNQAPPGLYTKTQDPAKAPN
          EFYN.FKGR.DLMEYA..HGIPI.VT.K.PW.MDENLMHIS.EAGILENPK.QAP.GLY.K.QDPAKAPN
Retrocopy EFYNQFKGRSDLMEYAEKHGIPIAVTLKHPWNMDENLMHISHEAGILENPKKQAPSGLYMKIQDPAKAPN

Parental  TPDILEIE-FKKG-VPVKVTNVKDGTTHQTSLELFMYLNEVAGKHGVGRIDIVENRFIGMKSRGIYETPA
          TPDI..IE..KKG.VPVKVT..KDGTTHQTSLELFMYLNEVAGKH.VG.IDIVENRFI.MKS.GI..TPA
Retrocopy TPDIFKIE<VKKG<VPVKVTSIKDGTTHQTSLELFMYLNEVAGKHSVGHIDIVENRFIEMKS*GICKTPA

Parental  GTILYHAHLDIEAFTMDREVRKIKQGLGLKFAELVYT
          GTILYH.HLDIEAFTM..EV.KIKQGLGLKFAELVYT
Retrocopy GTILYHSHLDIEAFTMEQEVHKIKQGLGLKFAELVYT

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	0.44 RPM	45.84 RPM
SRP007412_cerebellum	1.34 RPM	1.09 RPM
SRP007412_heart	0.18 RPM	5.81 RPM
SRP007412_kidney	0.63 RPM	673.87 RPM
SRP007412_liver	1.19 RPM	332.55 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1963 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1963 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1963 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2247
Pan troglodytes	retro_ptro_1590
Gorilla gorilla	retro_ggor_1675
Callithrix jacchus	retro_cjac_1219

---

Parental genes homology:

Parental genes homology involve 8 parental genes, and 68 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000020554	3 retrocopies	retro_cjac_1219, retro_cjac_4038, retro_cjac_4209,
Homo sapiens	ENSG00000130707	14 retrocopies	retro_hsap_2247, retro_hsap_2885, retro_hsap_3109, retro_hsap_3175, retro_hsap_3252, retro_hsap_3564, retro_hsap_3824, retro_hsap_4149, retro_hsap_4182, retro_hsap_4648, retro_hsap_4743, retro_hsap_4934, retro_hsap_820, retro_hsap_985,
Gorilla gorilla	ENSGGOG00000010228	8 retrocopies	retro_ggor_1346, retro_ggor_1675, retro_ggor_2134, retro_ggor_2403, retro_ggor_2574, retro_ggor_2787, retro_ggor_671, retro_ggor_787,
Myotis lucifugus	ENSMLUG00000006066	2 retrocopies	retro_mluc_1058, retro_mluc_1304,
Mus musculus	ENSMUSG00000076441	1 retrocopy	retro_mmus_135,
Nomascus leucogenys	ENSNLEG00000012500	13 retrocopies	retro_nleu_1088, retro_nleu_1245, retro_nleu_1317, retro_nleu_1381, retro_nleu_1390, retro_nleu_1424, retro_nleu_1701, retro_nleu_1792, retro_nleu_220, retro_nleu_253, retro_nleu_2680, retro_nleu_2764, retro_nleu_625,
Pongo abelii	ENSPPYG00000019692	13 retrocopies	retro_pabe_1963 , retro_pabe_2390, retro_pabe_2637, retro_pabe_2696, retro_pabe_2937, retro_pabe_3069, retro_pabe_3197, retro_pabe_3422, retro_pabe_3460, retro_pabe_3521, retro_pabe_3522, retro_pabe_731, retro_pabe_834,
Pan troglodytes	ENSPTRG00000021473	14 retrocopies	retro_ptro_1590, retro_ptro_1951, retro_ptro_2101, retro_ptro_2199, retro_ptro_2268, retro_ptro_2421, retro_ptro_2602, retro_ptro_2821, retro_ptro_2836, retro_ptro_3064, retro_ptro_3158, retro_ptro_3298, retro_ptro_571, retro_ptro_762,