RetrogeneDB ID: retro_hsap_4663

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: X:26766238..26767050(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000236683
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: HMGA1
• Ensembl ID: ENSG00000137309
• Aliases: HMGA1, HMG-R, HMGA1A, HMGIY
• Description: high mobility group AT-hook 1 [Source:HGNC Symbol;Acc:5010]

Sequence

>retro_hsap_4663
CAGCCTCTGGTGAGTCCCAGGACAGCGCTGGGAGGGAGTCAGAAGGAGCCCAGTGAAGTGCCAAAACCTAAGAGACCTCA
GGGCCGACCAAATGGAAGGAAAAACAAGGACGCTGCCAAGACCTGGAAAACCACCACAACTCCAGGAAGGAAACCAAGGG
GCAGACCCAAAAAACTGGAGAAGGAGGAAGAGGAGGGCATCTCACAGGAGTCCTCGGAGGAGGAGCAATGACCGTGCTTG
CGTGTCGCCTGCTCCTCACTGGAGGAGCAGCTTCCTTTTGGGACTGGACAGCTTTGCTCCGCTCCCACCGCCCCCGTCCC
TTCCCCAGGCCCACCATCACCACCGCCTCCAGCCGCCACCCCTGTCTTCCACCTGCGACTTCACCACCACACTACACAGC
ACACCAGCAGCTTCAGGGCCCCCATGGGCTGAGTGGGGAGCAGTTTTCCCCTGGCCTCAGTTCCCAGCTCCCCCCGCCCA
CCCACGCATACACATGTGCCCTCCTGGACAAGGCTAACGTTCCACTTAGCCGCACCCGGCACCTACTGCGTCCCCACTCC
TTTGGTGGTGGGGACATTGCTTTTTGGGCTTTTGGTTTGGGGGCGCCCTCTCTGCTCCTCCATTGTTCCCTCTGGCTTCC
CACAGTGGGGCCTGGGAGGGTTCCGCTGGCCTTAAAAGGGGCCCAAGCCCCATCTCATCCTGGCCTGCCCTACTCCACTG
CCCTGGCAGCAGCAGGTGTGGCCAATGGAGGGGGCTGCTGGCCCCCAGGATTCTACCAGCCAAGCTGTCTTCCTCACCAC
GTGGGGCTCACA

Alignment

ORF - retro_hsap_4663 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.1 %
• Parental protein coverage: 82.01 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QPLAS-KQEKDGTEKRGRGRPRKQPPVSPGTALVGSQKEPSEVPTPKRPRGRPKGSKNK-GEGGRGGHLA
          QPL.S..Q...G.E..G.....K....S..T.....Q............R...KG...K.GEGGRGGHL.
Retrocopy QPLVS<SQDSAGRESEGAQ*SAKT*ETSGPTKWKEKQGRCQDLENHHNSRKETKGQTQKTGEGGRGGHLT

Parental  GVLGGGAVTH-ACRLLLTGGAASFWDWTALLRSHRPHPFPRPTITTASGRHPHLPPVPSPPHYTAHQPLQ
          GVLGGGA.T..ACRLLLTGGAASFWDWTALLRSHRP.PFPRPTITTAS.RHP.LPP..SPPHYTAHQ.LQ
Retrocopy GVLGGGAMTVLACRLLLTGGAASFWDWTALLRSHRPRPFPRPTITTASSRHPCLPPATSPPHYTAHQQLQ

Parental  GSHGLSGEQFSPGLSSQLPPPTHAYTHALLDKANIPLSRTLHLLRPHSLGGGDIALWAFGLGAPSLLLHC
          G.HGLSGEQFSPGLSSQLPPPTHAYT.ALLDKAN.PLSRT.HLLRPHS.GGGDIA.WAFGLGAPSLLLHC
Retrocopy GPHGLSGEQFSPGLSSQLPPPTHAYTCALLDKANVPLSRTRHLLRPHSFGGGDIAFWAFGLGAPSLLLHC

Parental  SLWLPIVGPGRVPLALKGAQAPSHPGTPYSTALAAAGVANGGGCWPPGFPQPNCLCHHVGLT
          SLWLP.VGPGRVPLALKGAQAPSHPG.PYSTALAAAGVANGGGCWPPGF.QP.CL.HHVGLT
Retrocopy SLWLPTVGPGRVPLALKGAQAPSHPGLPYSTALAAAGVANGGGCWPPGFYQPSCLPHHVGLT

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	29.80 RPM
bodymap2_adrenal	0.00 RPM	22.37 RPM
bodymap2_brain	0.00 RPM	13.57 RPM
bodymap2_breast	0.00 RPM	16.17 RPM
bodymap2_colon	0.00 RPM	21.81 RPM
bodymap2_heart	0.00 RPM	15.71 RPM
bodymap2_kidney	0.00 RPM	8.36 RPM
bodymap2_liver	0.00 RPM	5.37 RPM
bodymap2_lung	0.00 RPM	68.62 RPM
bodymap2_lymph_node	0.00 RPM	49.23 RPM
bodymap2_ovary	0.00 RPM	5.96 RPM
bodymap2_prostate	0.00 RPM	19.02 RPM
bodymap2_skeletal_muscle	0.04 RPM	99.76 RPM
bodymap2_testis	0.00 RPM	98.55 RPM
bodymap2_thyroid	0.00 RPM	32.11 RPM
bodymap2_white_blood_cells	0.02 RPM	50.44 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_4663 was not detected

EST

No EST(s) were mapped for retro_hsap_4663 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_199122	961 libraries	586 libraries	269 libraries	11 libraries	2 libraries

The graphical summary, for retro_hsap_4663 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1829 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_hsap_4663 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_4663 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001061	1 retrocopy	retro_amel_1637,
Callithrix jacchus	ENSCJAG00000015226	2 retrocopies	retro_cjac_1197, retro_cjac_3158,
Homo sapiens	ENSG00000137309	4 retrocopies	retro_hsap_1175, retro_hsap_2277, retro_hsap_4663 , retro_hsap_695,
Myotis lucifugus	ENSMLUG00000010085	2 retrocopies	retro_mluc_1619, retro_mluc_2429,
Macaca mulatta	ENSMMUG00000019529	2 retrocopies	retro_mmul_1276, retro_mmul_2406,
Mus musculus	ENSMUSG00000046711	1 retrocopy	retro_mmus_188,
Nomascus leucogenys	ENSNLEG00000008303	1 retrocopy	retro_nleu_1097,
Pongo abelii	ENSPPYG00000029838	4 retrocopies	retro_pabe_1941, retro_pabe_2441, retro_pabe_3623, retro_pabe_960,
Pan troglodytes	ENSPTRG00000040884	6 retrocopies	retro_ptro_1611, retro_ptro_2053, retro_ptro_3098, retro_ptro_499, retro_ptro_789, retro_ptro_807,
Rattus norvegicus	ENSRNOG00000000488	1 retrocopy	retro_rnor_164,