RetrogeneDB ID: retro_hsap_3899

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 7:124940560..124940932(-)
• Located in intron of: ENSG00000237764

Retrocopy information

• Ensembl ID: ENSG00000213291
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPL31
• Ensembl ID: ENSG00000071082
• Aliases: RPL31, L31
• Description: ribosomal protein L31 [Source:HGNC Symbol;Acc:10334]

Sequence

>retro_hsap_3899
ATGGCTCCCGCAAAGAAGGGTGGCCAGAAGAAAAACGGCCATTCTGCCATCAACGAGGTGGTGACCCGAGAATACACCAT
CAATATTCCCAAGTGTGTCCATGGAGTGGGATTCAAGAAGCGTGCCCCTCGGGAACTCAGAGATTCCGCAATTTGCCATG
AAGGAGATGGGAACTCCTGATGTGCGCATTGATATGAGGCACAACAAAGTAGTCTGGGTAAAGGAGTAAGGGATGACCCA
TACCGTATCCGTGTGCGGTTGTCCAGAAAACGTAATGAGGATGAAAATTCACCAAGTAAGCTCTATACCTTGGTTACCTA
TGTACCTGTTACCACTTTCAAAAATCTACAGACAGTCAGTGTGGATGAGAAC

Alignment

ORF - retro_hsap_3899 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.56 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAPAKKGGEKKKGRSAINEVVTREYTINIHKRIHGV-GFKKRAPRALK-EIRKFAMKEMGTPDVRIDTRL
          MAPAKKGG.KK.G.SAINEVVTREYTINI.K..HGV.G.....P.....EI..FAMKEMGTPDVRID.R.
Retrocopy MAPAKKGGQKKNGHSAINEVVTREYTINIPKCVHGV<GIQEACPSGTQ<EIPQFAMKEMGTPDVRIDMRH

Parental  NKAVWAK-GIRNVPYRIRVRLSRKRNEDEDSPNKLYTLVTYVPVTTFKNLQTVNVDEN
          NK.VW.K.G.R..PYRIRVRLSRKRNEDE.SP.KLYTLVTYVPVTTFKNLQTV.VDEN
Retrocopy NKVVWVK<GVRDDPYRIRVRLSRKRNEDENSPSKLYTLVTYVPVTTFKNLQTVSVDEN

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	418.21 RPM
bodymap2_adrenal	0.00 RPM	617.22 RPM
bodymap2_brain	0.00 RPM	228.14 RPM
bodymap2_breast	0.00 RPM	375.16 RPM
bodymap2_colon	0.00 RPM	724.46 RPM
bodymap2_heart	0.00 RPM	197.05 RPM
bodymap2_kidney	0.00 RPM	276.37 RPM
bodymap2_liver	0.00 RPM	260.86 RPM
bodymap2_lung	0.00 RPM	734.42 RPM
bodymap2_lymph_node	0.00 RPM	777.29 RPM
bodymap2_ovary	0.00 RPM	734.99 RPM
bodymap2_prostate	0.00 RPM	913.89 RPM
bodymap2_skeletal_muscle	0.00 RPM	392.71 RPM
bodymap2_testis	0.00 RPM	430.21 RPM
bodymap2_thyroid	0.00 RPM	334.07 RPM
bodymap2_white_blood_cells	0.00 RPM	958.25 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_3899 was not detected

EST

No EST(s) were mapped for retro_hsap_3899 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_170468	347 libraries	418 libraries	969 libraries	81 libraries	14 libraries

The graphical summary, for retro_hsap_3899 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_3899 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3899 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 102 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000071082	45 retrocopies	retro_hsap_1026, retro_hsap_1056, retro_hsap_1075, retro_hsap_1102, retro_hsap_1118, retro_hsap_1150, retro_hsap_1217, retro_hsap_1269, retro_hsap_1345, retro_hsap_1527, retro_hsap_1691, retro_hsap_1856, retro_hsap_1865, retro_hsap_1993, retro_hsap_1998, retro_hsap_2215, retro_hsap_2246, retro_hsap_2388, retro_hsap_2470, retro_hsap_2510, retro_hsap_2610, retro_hsap_2615, retro_hsap_2627, retro_hsap_2839, retro_hsap_2921, retro_hsap_2959, retro_hsap_3108, retro_hsap_3325, retro_hsap_3471, retro_hsap_3472, retro_hsap_3525, retro_hsap_3731, retro_hsap_3777, retro_hsap_3788, retro_hsap_3899 , retro_hsap_3965, retro_hsap_4070, retro_hsap_4210, retro_hsap_461, retro_hsap_4693, retro_hsap_506, retro_hsap_548, retro_hsap_677, retro_hsap_794, retro_hsap_831,
Gorilla gorilla	ENSGGOG00000006432	24 retrocopies	retro_ggor_1047, retro_ggor_113, retro_ggor_1442, retro_ggor_169, retro_ggor_1811, retro_ggor_1839, retro_ggor_192, retro_ggor_1971, retro_ggor_21, retro_ggor_2132, retro_ggor_2383, retro_ggor_2541, retro_ggor_2547, retro_ggor_2625, retro_ggor_2820, retro_ggor_442, retro_ggor_583, retro_ggor_655, retro_ggor_834, retro_ggor_84, retro_ggor_849, retro_ggor_874, retro_ggor_88, retro_ggor_997,
Latimeria chalumnae	ENSLACG00000013603	1 retrocopy	retro_lcha_94,
Macropus eugenii	ENSMEUG00000000963	8 retrocopies	retro_meug_1083, retro_meug_1433, retro_meug_1731, retro_meug_1741, retro_meug_198, retro_meug_418, retro_meug_588, retro_meug_649,
Myotis lucifugus	ENSMLUG00000002507	21 retrocopies	retro_mluc_1072, retro_mluc_1135, retro_mluc_1239, retro_mluc_1301, retro_mluc_1406, retro_mluc_1470, retro_mluc_1666, retro_mluc_1678, retro_mluc_1896, retro_mluc_1913, retro_mluc_2028, retro_mluc_2124, retro_mluc_2126, retro_mluc_269, retro_mluc_303, retro_mluc_463, retro_mluc_767, retro_mluc_782, retro_mluc_914, retro_mluc_922, retro_mluc_997,
Macaca mulatta	ENSMMUG00000009873	1 retrocopy	retro_mmul_340,
Nomascus leucogenys	ENSNLEG00000014444	2 retrocopies	retro_nleu_47, retro_nleu_530,