RetrogeneDB ID: retro_hsap_1472

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 15:30336925..30337495(+)
• Located in intron of: ENSG00000259647

Retrocopy information

• Ensembl ID: ENSG00000260174
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SYNGR2
• Ensembl ID: ENSG00000108639
• Aliases: None
• Description: synaptogyrin 2 [Source:HGNC Symbol;Acc:11499]

Sequence

>retro_hsap_1472
GTCTTCGCCTTGATCGTGTTCTCCTGCATCTATGGCGAGGGCTACAGCAACACCCATAAGTCTAAGCAGATGTACTGCGT
GTTCAACCACAACGAGGATGCCTGCCGCTATGGCAGTGCCATCGGGGTGCTGGCCTTCCTGGCCTCGGCCTTCTTGGTGG
TCGACGCGTATTTCCCCCAGATCAGCAACGCCACTGACCGCAAGTACCTCGTCATTGGTGACCTGCTCTTTTCAGCTCTC
TGGACCTTCCTGTGGTTTGTTGGTTTCTGCTTCCTCACCAACCAGTGGGCGGTCACCGACCCGGAGGACGTGCTGGTGGG
GGCCGACTCTGCGAGGGCAGCCATCACCTTCAGCTTCTTTTCCATCTTCTCCTGGGGTGTGCTGGCCTCCCTGACCTACC
AGCGCTACAAGGCTGGCGTGGACGACTTCATCCAGAACTACGTCGACCCCAGTCCGGACCCCAACACTGCCTACGCCTCC
TACCCAGGTGCATCTGTGGACAACTACCAACAGCCACCCTTCACCCAGAATGCGGAGACCACCGAGGGCTACCAGCCGCC
CCCTGTGTAC

Alignment

ORF - retro_hsap_1472 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.29 %
• Parental protein coverage: 85.27 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VFALIVFSCIYGEGYSNAHESKQMYCVFNRNEDACRYGSAIGVLAFLASAFFLVVDAYFPQISNATDRKY
          VFALIVFSCIYGEGYSN.H.SKQMYCVFN.NEDACRYGSAIGVLAFLASA.FLVVDAYFPQISNATDRKY
Retrocopy VFALIVFSCIYGEGYSNTHKSKQMYCVFNHNEDACRYGSAIGVLAFLASA-FLVVDAYFPQISNATDRKY

Parental  LVIGDLLFSALWTFLWFVGFCFLTNQWAVTNPKDVLVGADSVRAAITFSFFSIFSWGVLASLAYQRYKAG
          LVIGDLLFSALWTFLWFVGFCFLTNQWAVT.P.DVLVGADS.RAAITFSFFSIFSWGVLASL.YQRYKAG
Retrocopy LVIGDLLFSALWTFLWFVGFCFLTNQWAVTDPEDVLVGADSARAAITFSFFSIFSWGVLASLTYQRYKAG

Parental  VDDFIQNYVDPTPDPNTAYASYPGASVDNYQQPPFTQNAETTEGYQPPPVY
          VDDFIQNYVDP.PDPNTAYASYPGASVDNYQQPPFTQNAETTEGYQPPPVY
Retrocopy VDDFIQNYVDPSPDPNTAYASYPGASVDNYQQPPFTQNAETTEGYQPPPVY

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	37.71 RPM
bodymap2_adrenal	0.00 RPM	71.75 RPM
bodymap2_brain	0.00 RPM	11.11 RPM
bodymap2_breast	0.00 RPM	34.88 RPM
bodymap2_colon	0.00 RPM	33.64 RPM
bodymap2_heart	0.00 RPM	37.99 RPM
bodymap2_kidney	0.00 RPM	45.06 RPM
bodymap2_liver	0.00 RPM	33.67 RPM
bodymap2_lung	0.00 RPM	142.88 RPM
bodymap2_lymph_node	0.02 RPM	76.18 RPM
bodymap2_ovary	0.02 RPM	26.54 RPM
bodymap2_prostate	0.02 RPM	54.92 RPM
bodymap2_skeletal_muscle	0.29 RPM	178.02 RPM
bodymap2_testis	0.40 RPM	18.89 RPM
bodymap2_thyroid	0.09 RPM	34.48 RPM
bodymap2_white_blood_cells	0.02 RPM	92.10 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_1472 was not detected

EST

No EST(s) were mapped for retro_hsap_1472 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_42580	869 libraries	677 libraries	269 libraries	9 libraries	5 libraries
TSS #2	TSS_42581	1823 libraries	4 libraries	2 libraries	0 libraries	0 libraries

The graphical summary, for retro_hsap_1472 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_1472 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_1472 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000108639	2 retrocopies	retro_hsap_1472 , retro_hsap_4275,
Macaca mulatta	ENSMMUG00000021864	1 retrocopy	retro_mmul_1200,
Pongo abelii	ENSPPYG00000008684	2 retrocopies	retro_pabe_1220, retro_pabe_3487,
Ictidomys tridecemlineatus	ENSSTOG00000006834	1 retrocopy	retro_itri_705,