RetrogeneDB ID: retro_hsap_4657

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: X:23093874..23094459(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000174028
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: FAM3C
• Ensembl ID: ENSG00000196937
• Aliases: FAM3C, ILEI
• Description: family with sequence similarity 3, member C [Source:HGNC Symbol;Acc:18664]

Sequence

>retro_hsap_4657
ATGAGGGTAGCAGGTGCTGCAAAGTTGGTGGTAGCTGTGGCAGTGTTTTTACTGACATTTTATGTTATTTCTCAAGTATT
TGAAATAAAAATGGATGCAAGTTTAGGAAATCTATTTGCAAGATCAGCATTGGACACAGCTGCACGTTCTACAAAGCCTC
CCAGATATAAGTGTGGGATCTCAAAAGCTTGCCCTGAGAAGCATTTTGCTTTTAAAATGGCAAGTGGAGCAGCCAACGTG
GTGGGACCCAAAATCTGCCTGGAAGATAATGTTTTAATGAGTGGTGTTAAGAATAATGTTGGAAGAGGGATCAATGTTGC
CTTGGCAAATGGAAAAACAGGAGAAGTATTAGACACTAAATATTTTGACATGTGGGGAGGAGATGTGGCACCATTTATTG
AGTTTCTGAAGGCCATACAAGATGGAACAATAGTTTTAATGGGAACATACGATGATGGAGCAACCAAACTCAATGATGAG
GCACGGCGGCTCATTGCTGATTTGGGGAGCACATCTATTACTAATCTTGGTTTTAGAGACAACTGGGTCTTCTGTGGTGG
GAAGGGCATTAAGACAAAAAGCCCT

Alignment

ORF - retro_hsap_4657 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100.0 %
• Parental protein coverage: 85.9 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MRVAGAAKLVVAVAVFLLTFYVISQVFEIKMDASLGNLFARSALDTAARSTKPPRYKCGISKACPEKHFA
          MRVAGAAKLVVAVAVFLLTFYVISQVFEIKMDASLGNLFARSALDTAARSTKPPRYKCGISKACPEKHFA
Retrocopy MRVAGAAKLVVAVAVFLLTFYVISQVFEIKMDASLGNLFARSALDTAARSTKPPRYKCGISKACPEKHFA

Parental  FKMASGAANVVGPKICLEDNVLMSGVKNNVGRGINVALANGKTGEVLDTKYFDMWGGDVAPFIEFLKAIQ
          FKMASGAANVVGPKICLEDNVLMSGVKNNVGRGINVALANGKTGEVLDTKYFDMWGGDVAPFIEFLKAIQ
Retrocopy FKMASGAANVVGPKICLEDNVLMSGVKNNVGRGINVALANGKTGEVLDTKYFDMWGGDVAPFIEFLKAIQ

Parental  DGTIVLMGTYDDGATKLNDEARRLIADLGSTSITNLGFRDNWVFCGGKGIKTKSP
          DGTIVLMGTYDDGATKLNDEARRLIADLGSTSITNLGFRDNWVFCGGKGIKTKSP
Retrocopy DGTIVLMGTYDDGATKLNDEARRLIADLGSTSITNLGFRDNWVFCGGKGIKTKSP

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	1.19 RPM	26.28 RPM
bodymap2_adrenal	1.60 RPM	52.42 RPM
bodymap2_brain	5.09 RPM	134.76 RPM
bodymap2_breast	1.05 RPM	27.32 RPM
bodymap2_colon	2.05 RPM	42.81 RPM
bodymap2_heart	0.89 RPM	35.87 RPM
bodymap2_kidney	2.83 RPM	72.82 RPM
bodymap2_liver	0.93 RPM	38.57 RPM
bodymap2_lung	1.51 RPM	60.34 RPM
bodymap2_lymph_node	1.37 RPM	57.64 RPM
bodymap2_ovary	1.54 RPM	42.70 RPM
bodymap2_prostate	1.00 RPM	35.04 RPM
bodymap2_skeletal_muscle	0.27 RPM	9.84 RPM
bodymap2_testis	1.19 RPM	47.26 RPM
bodymap2_thyroid	5.24 RPM	91.37 RPM
bodymap2_white_blood_cells	0.43 RPM	18.47 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_4657 was not detected

EST

No EST(s) were mapped for retro_hsap_4657 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_198974	1062 libraries	318 libraries	412 libraries	30 libraries	7 libraries
TSS #2	TSS_198975	784 libraries	800 libraries	232 libraries	9 libraries	4 libraries
TSS #3	TSS_198976	1193 libraries	570 libraries	64 libraries	1 library	1 library
TSS #4	TSS_198977	973 libraries	711 libraries	138 libraries	7 libraries	0 libraries

The graphical summary, for retro_hsap_4657 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_4657 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_4657 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003224	1 retrocopy	retro_chof_1467,
Felis catus	ENSFCAG00000023087	1 retrocopy	retro_fcat_1392,
Homo sapiens	ENSG00000196937	1 retrocopy	retro_hsap_4657 ,
Loxodonta africana	ENSLAFG00000010029	1 retrocopy	retro_lafr_1169,
Macropus eugenii	ENSMEUG00000006906	2 retrocopies	retro_meug_2057, retro_meug_536,
Monodelphis domestica	ENSMODG00000015478	1 retrocopy	retro_mdom_1392,
Sarcophilus harrisii	ENSSHAG00000015103	1 retrocopy	retro_shar_6,
Tursiops truncatus	ENSTTRG00000016229	2 retrocopies	retro_ttru_1219, retro_ttru_855,