RetrogeneDB ID: retro_hsap_3100

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 4:139402409..139403250(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000248305
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ARMC1
• Ensembl ID: ENSG00000104442
• Aliases: ARMC1, Arcp
• Description: armadillo repeat containing 1 [Source:HGNC Symbol;Acc:17684]

Sequence

>retro_hsap_3100
ATGAATTCTTCCACCTCCACCATGAATGAAGAGTCTGATACTCTATCGGTAGTTAACCAGTTAGGGGATATAGCAGCAGA
TCCATTAAACAGAAGAGCTGTAGTCCAGGATCAGGGATGTCTGCCTTGCCTTATTTTATTTATGGACCACCCCAACCCTC
CAGTCCATTTGGCTTTGCTCGCTCTTTGATACTTGGGAGAACACCGTGCAAACAGAGAAAAGATGAAAGGAGAACTGGGT
ATGATGTTGAGCCTACAAAATGTTATACAGAAAACTGCAACTCTGGGAGAAACAAAACTTCTGGCCTCTGAAATCTATGA
CATACTTCAGTCCTCCAATAAGGCAGATGGTGATAGTTTCAATGAAATGAATTCATATTGAAGGAAAGCTCAGTTTTTTC
TGGGAACTGCAAACAAACGTGCCAAAACAGTGGTTTTGCATATAGACGGCCTTGATGATACGTCTTCGAGAAATCTATAT
GAAGAGGCTTTGTTAAAAATTAAAGGTGTTATTAGCTTTACTTTTCAAATGGCTGTTCAAAGGCTTGGTGTGAATCCGTT
CAGATTTGAAAGCTGAGGCTTTCGCATCAGCGAGAGCATCAACCAAGGTTATGAAAGCTCCGTAAGTTGTGAAAAGTGAA
AGTGGAGAAGAGATGCTGGTCCCATTCCAAGACCTTCCTGTGGTAGAACAGAACACAGAGCTACCTGACTACCTGTCTGA
AGATGAGAGTCCCACAAATGAACAGTACAAGGTGGTGTCCTGGGTCTTCAGCTCACACCCAGTGGGTGGAACTAGCTGGC
TGAGCACAGCTGCAAACTTTTTATCCAGATCGTTTTATTGG

Alignment

ORF - retro_hsap_3100 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.04 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MNSSTSTMSEEPDALSVVNQLRDLAADPLNRRAIVQDQGCLPGLILFMDHPNPPVVHSALLALRYLAECR
          MNSSTSTM.EE.D.LSVVNQL.D.AADPLNRRA.VQDQGCLP.LILFMDHPNPPV.H.ALLAL.YL.E.R
Retrocopy MNSSTSTMNEESDTLSVVNQLGDIAADPLNRRAVVQDQGCLPCLILFMDHPNPPV-HLALLAL*YLGEHR

Parental  ANREKMKGELGMMLSLQNVIQKTTTPGETKLLASEIYDILQSSNMADGDSFNEMNSRRRKAQFFLGTTNK
          ANREKMKGELGMMLSLQNVIQKT.T.GETKLLASEIYDILQSSN.ADGDSFNEMNS..RKAQFFLGT.NK
Retrocopy ANREKMKGELGMMLSLQNVIQKTATLGETKLLASEIYDILQSSNKADGDSFNEMNSY*RKAQFFLGTANK

Parental  RAKTVVLHIDGLDDTSRRNLCEEALLKI-KGVISFTFQMAVQRCVVRIRSDLKAEALASAIASTKVMKAQ
          RAKTVVLHIDGLDDTS.RNL.EEALLKI.K......F........V.IRSDLKAEA.ASA.ASTKVMKA.
Retrocopy RAKTVVLHIDGLDDTSSRNLYEEALLKI>KVLLALLFKWLFKG-LV*IRSDLKAEAFASARASTKVMKAP

Parental  QVVKSESGEEMLVPFQDTPVEVEQNTELPDYLPEDESPTKEQDKAVSRV-GSHPEGGASWLSTAANFLSR
          .VVKSESGEEMLVPFQD.PV.VEQNTELPDYL.EDESPT.EQ.K.VS.V..SHP.GG.SWLSTAANFLSR
Retrocopy *VVKSESGEEMLVPFQDLPV-VEQNTELPDYLSEDESPTNEQYKVVSWVFSSHPVGGTSWLSTAANFLSR

Parental  SFYW
          SFYW
Retrocopy SFYW

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	29.86 RPM
bodymap2_adrenal	0.00 RPM	42.68 RPM
bodymap2_brain	0.00 RPM	59.42 RPM
bodymap2_breast	0.04 RPM	41.50 RPM
bodymap2_colon	0.00 RPM	50.04 RPM
bodymap2_heart	0.00 RPM	34.80 RPM
bodymap2_kidney	0.00 RPM	46.22 RPM
bodymap2_liver	0.00 RPM	22.86 RPM
bodymap2_lung	0.00 RPM	18.23 RPM
bodymap2_lymph_node	0.00 RPM	33.88 RPM
bodymap2_ovary	0.02 RPM	51.49 RPM
bodymap2_prostate	0.00 RPM	58.13 RPM
bodymap2_skeletal_muscle	0.00 RPM	35.58 RPM
bodymap2_testis	0.00 RPM	43.81 RPM
bodymap2_thyroid	0.00 RPM	44.76 RPM
bodymap2_white_blood_cells	0.00 RPM	44.20 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_3100 was not detected

EST

No EST(s) were mapped for retro_hsap_3100 retrocopy.

TSS

No TSS is located nearby retro_hsap_3100 retrocopy 5' end.

Lab

retro_hsap_3100 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3100 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000015901	1 retrocopy	retro_btau_1447,
Homo sapiens	ENSG00000104442	1 retrocopy	retro_hsap_3100 ,
Gorilla gorilla	ENSGGOG00000022803	1 retrocopy	retro_ggor_2129,
Myotis lucifugus	ENSMLUG00000014037	1 retrocopy	retro_mluc_2058,
Nomascus leucogenys	ENSNLEG00000003916	1 retrocopy	retro_nleu_1518,
Oryctolagus cuniculus	ENSOCUG00000000392	2 retrocopies	retro_ocun_1437, retro_ocun_782,
Pongo abelii	ENSPPYG00000018630	1 retrocopy	retro_pabe_2474,
Pan troglodytes	ENSPTRG00000020298	1 retrocopy	retro_ptro_2096,
Sus scrofa	ENSSSCG00000006220	1 retrocopy	retro_sscr_1027,