RetrogeneDB ID: retro_hsap_4743

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: X:114899214..114900450(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000227881
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ASS1
• Ensembl ID: ENSG00000130707
• Aliases: ASS1, ASS, CTLN1
• Description: argininosuccinate synthase 1 [Source:HGNC Symbol;Acc:758]

Sequence

>retro_hsap_4743
ATGTCCAGCAAAGGCTCTGTGGTTCTGGCCTACAGTGGCGGCCTGGACACCTCCTGCATCCTCGTGTTACTGAAGGAACA
AGGCTATGACATCATTGCCTACGTGGCCAACACTGGCCAGAAGGAAGACTTTGAGGAAGCCAGGAAGAAGGCACTGAAGC
TTGGGGGCAAAAAGGTGTTCATTGAGGAAGTCAGCAAGGAGTTTGTGAAGGAGTTCATCTGGCTGGCCATCCAGTCCAGC
GCACTGTATGAGGACCACTACCTCCTGGGCACCTCTCTCACCAGGCCCTGCATCGCCCGAAAACAAGTGGAAATCGCCCA
GCAGGAGAGGGCCAAGTAAGTGTCCCACAGCGCCACAGGAAAGGGAAATGATCAGGTCCAGTTTGAGCTAAACTGCTACT
CTCTGGCCCCCCCAGATAAAGGTCATTGCTCCCTGGAGGATGCCCAAGTTCTACAACAGGTTCAAGGTCCGAAATGACCT
TATGGAACACACAAAGCAACACGGGATTCCCATCCCAGTCACTCCCAAGAACCTGTGGAACATGGACGAGAACCTCATGC
AGATCAGCAATGAGGCTGGAATCTTGGAGAACCCTAAGAACCAAGCATTTCCAGGTCTCTCCACGAAGACCCAGGACCCG
GCCAAAGCCCCCAGAACCCCTGACATTCTCGAGATCGAGTTCAAATAAGGAGTCCCCATGAAAGTGACCAACGTCAAGGA
TGGCACCACCCACCAGACCTCCTTGGAGCTCTTCCTGTACCTGAACGAAGACGTGGGCAAGTACAGCTTGGGCCGTATTG
ACATCAAGGAGAACCACTTCACTGGAATGAAGTCCCCAGGTATCTATGAGACCCCAGCAGACACCATCGTTTACCATGCT
CATTTAGACATCAGGGCCTTCACCATGGACCGGGAAGTATGCAAAATCAAATAAGGCCTGGGCTTGAAATTTGCTGAGCT
GGTGTATACCGGTTTCTGGCACAGCCTTGAGTGTAAATTTGTCCACCACTGCATTGCCAAGTCCCAGGAGTGAGTGGAAG
GGAAAGTGCAGGTGTCCGTCTTCAAGGGCCTGGTGTACATCCTAGGCCAGGAGTCCCTCTGTTTATCTACAACGAGGAGC
TGGTGAGCATGAACGTGCAGGTTGATTATGAGCCAATCGATGCCACCAGTTTCATCAACATCAATTCCCTCAGGCTGAAG
GAATATCATCATCTCCAGAGCAAGGTCACTGCCAAA

Alignment

ORF - retro_hsap_4743 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.51 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSSKGSVVLAYSGGLDTSCILVWLKEQGYDVIAYLANIGQKEDFEEARKKALKLGAKKVFIEDVSREFVE
          MSSKGSVVLAYSGGLDTSCILV.LKEQGYD.IAY.AN.GQKEDFEEARKKALKLG.KKVFIE.VS.EFV.
Retrocopy MSSKGSVVLAYSGGLDTSCILVLLKEQGYDIIAYVANTGQKEDFEEARKKALKLGGKKVFIEEVSKEFVK

Parental  EFIWPAIQSSALYEDRYLLGTSLARPCIARKQVEIAQREGAKYVSHGATGKGNDQVRFELSCYSLAP-QI
          EFIW.AIQSSALYED.YLLGTSL.RPCIARKQVEIAQ.E.AK.VSH.ATGKGNDQV.FEL.CYSLAP.QI
Retrocopy EFIWLAIQSSALYEDHYLLGTSLTRPCIARKQVEIAQQERAK*VSHSATGKGNDQVQFELNCYSLAP>QI

Parental  KVIAPWRMPEFYNRFKGRNDLMEYAKQHGIPIPVTPKNPWSMDENLMHISYEAGILENPKNQAPPGLYTK
          KVIAPWRMP.FYNRFK.RNDLME..KQHGIPIPVTPKN.W.MDENLM.IS.EAGILENPKNQA.PGL.TK
Retrocopy KVIAPWRMPKFYNRFKVRNDLMEHTKQHGIPIPVTPKNLWNMDENLMQISNEAGILENPKNQAFPGLSTK

Parental  TQDPAKAPNTPDILEIEFKKGVPVKVTNVKDGTTHQTSLELFMYLNEVAGKHGVGRIDIVENRFIGMKSR
          TQDPAKAP.TPDILEIEFK.GVP.KVTNVKDGTTHQTSLELF.YLNE..GK...GRIDI.EN.F.GMKS.
Retrocopy TQDPAKAPRTPDILEIEFK*GVPMKVTNVKDGTTHQTSLELFLYLNEDVGKYSLGRIDIKENHFTGMKSP

Parental  GIYETPAGTILYHAHLDIEAFTMDREVRKIKQGLGLKFAELVYTGFWHSPECEFVRHCIAKSQERVEGKV
          GIYETPA.TI.YHAHLDI.AFTMDREV.KIK.GLGLKFAELVYTGFWHS.EC.FV.HCIAKSQE.VEGKV
Retrocopy GIYETPADTIVYHAHLDIRAFTMDREVCKIK*GLGLKFAELVYTGFWHSLECKFVHHCIAKSQE*VEGKV

Parental  QVSVLKGQVYILGRES-PLSLYNEELVSMNVQGDYEPTDATGFININSLRLKEYHRLQSKVTAK
          QVSV.KG.VYILG.ES.PL..YNEELVSMNVQ.DYEP.DAT.FININSLRLKEYH.LQSKVTAK
Retrocopy QVSVFKGLVYILGQES<PLFIYNEELVSMNVQVDYEPIDATSFININSLRLKEYHHLQSKVTAK

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	238.28 RPM
bodymap2_adrenal	0.00 RPM	46.81 RPM
bodymap2_brain	0.00 RPM	23.44 RPM
bodymap2_breast	0.00 RPM	183.45 RPM
bodymap2_colon	0.00 RPM	77.38 RPM
bodymap2_heart	0.00 RPM	33.05 RPM
bodymap2_kidney	0.19 RPM	245.71 RPM
bodymap2_liver	0.00 RPM	432.27 RPM
bodymap2_lung	0.07 RPM	79.76 RPM
bodymap2_lymph_node	0.04 RPM	41.15 RPM
bodymap2_ovary	0.02 RPM	93.22 RPM
bodymap2_prostate	0.00 RPM	119.92 RPM
bodymap2_skeletal_muscle	0.00 RPM	31.65 RPM
bodymap2_testis	0.00 RPM	118.38 RPM
bodymap2_thyroid	0.00 RPM	69.49 RPM
bodymap2_white_blood_cells	0.00 RPM	0.18 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_4743 was not detected

EST

No EST(s) were mapped for retro_hsap_4743 retrocopy.

TSS

No TSS is located nearby retro_hsap_4743 retrocopy 5' end.

Lab

retro_hsap_4743 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_4743 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_3158

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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,