RetrogeneDB ID: retro_hsap_3626

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 6:86880161..86880519(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000217272
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RAB1A
• Ensembl ID: ENSG00000138069
• Aliases: RAB1A, RAB1, YPT1
• Description: RAB1A, member RAS oncogene family [Source:HGNC Symbol;Acc:9758]

Sequence

>retro_hsap_3626
CACAGGAGCCTAAGGCTGTATGATATGACAGATCAGGAGTCCTTCGATAATGTCAAATAGTGGTTGCAGGAAATTGATCA
CTAGGCCAGTGAAAATGTCAACAAATTGTTGGTAGGAAACAAATGTGATTGCCCACAAAGAAAGTAGACTACACAACAAC
AAAGGAATTTGCTGATTCCCTTGGAATTCCATTTTTGGAAACTGGTGCTAAGAACACAGCAAATGTAGAACAGACTTTCA
TGAAAATGGCATCTGAGATTAAAAAGCAAATGGGACTAGAGCAACAGCTGGTGATGCAGAGAAGTCTAATTTTAAAATTT
AGACCACTTTGGTCAAGCAGTCAGGTGAAGGTTGATGC

Alignment

ORF - retro_hsap_3626 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.8 %
• Parental protein coverage: 69.94 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  HGIIVVYDVTDQESFNNVKQWLQEIDRYASENVNKLLVGNKCD-LTTKKVVDYTTAKEFADSLGIPFLET
          H.....YD.TDQESF.NVK.WLQEID..ASENVNKLLVGNKCD.L.TKKV.DYTT.KEFADSLGIPFLET
Retrocopy HRSLRLYDMTDQESFDNVK*WLQEIDH*ASENVNKLLVGNKCD<LPTKKV-DYTTTKEFADSLGIPFLET

Parental  SAKNATNVEQSFMTMAAEIKKRM-GPGATAGGAEKSNVKIQSTPVKQSGGGCC
          .AKN..NVEQ.FM.MA.EIKK.M.G..ATAG.AEKSN.KI..T.VKQSG.G.C
Retrocopy GAKNTANVEQTFMKMASEIKKQM<GTRATAGDAEKSNFKI*TTLVKQSGEG*C

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	155.62 RPM
bodymap2_adrenal	0.00 RPM	128.40 RPM
bodymap2_brain	0.00 RPM	148.66 RPM
bodymap2_breast	0.00 RPM	170.24 RPM
bodymap2_colon	0.00 RPM	165.26 RPM
bodymap2_heart	0.00 RPM	104.88 RPM
bodymap2_kidney	0.00 RPM	245.15 RPM
bodymap2_liver	0.00 RPM	140.41 RPM
bodymap2_lung	0.00 RPM	207.52 RPM
bodymap2_lymph_node	0.00 RPM	132.43 RPM
bodymap2_ovary	0.04 RPM	169.58 RPM
bodymap2_prostate	0.00 RPM	156.00 RPM
bodymap2_skeletal_muscle	0.00 RPM	50.18 RPM
bodymap2_testis	0.00 RPM	163.53 RPM
bodymap2_thyroid	0.00 RPM	197.88 RPM
bodymap2_white_blood_cells	0.00 RPM	112.56 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_3626 was not detected

EST

No EST(s) were mapped for retro_hsap_3626 retrocopy.

TSS

No TSS is located nearby retro_hsap_3626 retrocopy 5' end.

Lab

retro_hsap_3626 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3626 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 11 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000002205	2 retrocopies	retro_etel_1687, retro_etel_413,
Homo sapiens	ENSG00000138069	2 retrocopies	retro_hsap_2362, retro_hsap_3626 ,
Homo sapiens	ENSG00000143545	1 retrocopy	retro_hsap_1122,
Homo sapiens	ENSG00000174903	1 retrocopy	retro_hsap_4252,
Macaca mulatta	ENSMMUG00000021721	1 retrocopy	retro_mmul_951,
Oryctolagus cuniculus	ENSOCUG00000017003	1 retrocopy	retro_ocun_800,
Pongo abelii	ENSPPYG00000012360	1 retrocopy	retro_pabe_2135,
Pan troglodytes	ENSPTRG00000011989	1 retrocopy	retro_ptro_1727,
Rattus norvegicus	ENSRNOG00000004992	1 retrocopy	retro_rnor_110,
Ictidomys tridecemlineatus	ENSSTOG00000020693	1 retrocopy	retro_itri_1541,
Drosophila melanogaster	FBgn0016700	1 retrocopy	retro_dmel_36,