RetrogeneDB ID: retro_hsap_1259

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 13:45964488..45965468(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000214455
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RCN1
• Ensembl ID: ENSG00000049449
• Aliases: RCN1, HEL-S-84, PIG20, RCAL, RCN
• Description: reticulocalbin 1, EF-hand calcium binding domain [Source:HGNC Symbol;Acc:9934]

Sequence

>retro_hsap_1259
CGCGGTGGCCGCCTGGGGTTAGCCCTGGGGCTGCTGCTGGCGCTGGTGCTGGCGCCGCGGGTTCTGCGGGCCAAGCCCAC
GGTGCGCAAAGAGCGCGTGGTGCGGCCCGACTCGGAGCTGGGCGAGCGGCCCCCTGAGGACAACCAGAGCTTCCAGTACG
ACCACGAGGCCTTCCTGGGCAAGGAGGACTCCAAGAACTTCGACGAGCTCACCCCGGACGAGAGCAAGGAGAGGCTAGGG
AAGATTGTTGATCGAATCGACAATGATGGGTATGGCTTTGTCACTACTGAGGAGCTGAAAACCTGGATCAAACGGGTGCA
GAAAAGATACATCTTTGATAATGTCGCCAAAGTCTGGAAGGATTATGATAGGGACAAGGATGATAACATTTCCTGGGAAG
AATACAAACAAGCCACCTATGGTTACTATACCTAGGAAACCCCGCAGAGTTTCATGATTCTTCAGATCATCACACCTTTA
AAAAGATGCTGCCACGTGATGAGAGAAGATTCAAAGCTGCAGACCTCAATGGTGACCTGACAGCTACTCCGGAGGAGTTC
ACTGCCTTTCTGCATCCTGAAGAGTTTGAACATATGAAGGAAATTGTGGCTTTGGAAACCCTGGAGGACATCGACAAGAA
CGGGGATGGGTTTGTGGATCAGGATGAGTATATTGCGGATATGTTTTCCCATGAGGAGAATGGCCCTGAGCCAGACTGGG
TTTTATCAGAACGGGAGCAGTTTAACGAATTCCGGGATCTGAACAAGGACGGGAAGTTAGACAAAGATGAGATTCGCCAC
TGGATCCTCCCTCAAGATTATGATCATGCACAGGCTGAGGCCAGGCATCTGGTATATGAGTCAGACAAAAACAAGGATGA
GAAGCTAACTAAAGAGGAAATATTGGAGAACTGGAACATGTTTGTTGGAAGCCAAGCTACCAATTACGGGGAAGATCTCA
CAAAAAATCATGATGAGCTT

Alignment

ORF - retro_hsap_1259 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.73 %
• Parental protein coverage: 98.49 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RGRRLGLALGLLLALVLAPRVLRAKPTVRKERVVRPDSELGERPPEDNQSFQYDHEAFLGKEDSKTFDQL
          RG.RLGLALGLLLALVLAPRVLRAKPTVRKERVVRPDSELGERPPEDNQSFQYDHEAFLGKEDSK.FD.L
Retrocopy RGGRLGLALGLLLALVLAPRVLRAKPTVRKERVVRPDSELGERPPEDNQSFQYDHEAFLGKEDSKNFDEL

Parental  TPDESKERLGKIVDRIDNDGDGFVTTEELKTWIKRVQKRYIFDNVAKVWKDYDRDKDDKISWEEYKQATY
          TPDESKERLGKIVDRIDNDG.GFVTTEELKTWIKRVQKRYIFDNVAKVWKDYDRDKDD.ISWEEYKQATY
Retrocopy TPDESKERLGKIVDRIDNDGYGFVTTEELKTWIKRVQKRYIFDNVAKVWKDYDRDKDDNISWEEYKQATY

Parental  GYYL-GNPAEF-HDSSDHHTFKKMLPRDERRFKAADLNGDLTATREEFTAFLHPEEFEHMKEIVVLETLE
          GYY....P..F.HDSSDHHTFKKMLPRDERRFKAADLNGDLTAT.EEFTAFLHPEEFEHMKEIV.LETLE
Retrocopy GYYT*ETPQSF<HDSSDHHTFKKMLPRDERRFKAADLNGDLTATPEEFTAFLHPEEFEHMKEIVALETLE

Parental  DIDKNGDGFVDQDEYIADMFSHEENGPEPDWVLSEREQFNEFRDLNKDGKLDKDEIRHWILPQDYDHAQA
          DIDKNGDGFVDQDEYIADMFSHEENGPEPDWVLSEREQFNEFRDLNKDGKLDKDEIRHWILPQDYDHAQA
Retrocopy DIDKNGDGFVDQDEYIADMFSHEENGPEPDWVLSEREQFNEFRDLNKDGKLDKDEIRHWILPQDYDHAQA

Parental  EARHLVYESDKNKDEKLTKEEILENWNMFVGSQATNYGEDLTKNHDEL
          EARHLVYESDKNKDEKLTKEEILENWNMFVGSQATNYGEDLTKNHDEL
Retrocopy EARHLVYESDKNKDEKLTKEEILENWNMFVGSQATNYGEDLTKNHDEL

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	27.01 RPM	166.62 RPM
bodymap2_adrenal	2.29 RPM	156.06 RPM
bodymap2_brain	6.00 RPM	50.54 RPM
bodymap2_breast	9.69 RPM	102.80 RPM
bodymap2_colon	9.78 RPM	151.48 RPM
bodymap2_heart	3.30 RPM	35.96 RPM
bodymap2_kidney	8.89 RPM	98.38 RPM
bodymap2_liver	4.60 RPM	67.68 RPM
bodymap2_lung	5.47 RPM	113.40 RPM
bodymap2_lymph_node	6.19 RPM	95.00 RPM
bodymap2_ovary	4.47 RPM	239.25 RPM
bodymap2_prostate	8.83 RPM	128.97 RPM
bodymap2_skeletal_muscle	1.04 RPM	27.94 RPM
bodymap2_testis	4.73 RPM	137.82 RPM
bodymap2_thyroid	11.49 RPM	151.84 RPM
bodymap2_white_blood_cells	0.65 RPM	16.32 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_1259 was not detected

EST

No EST(s) were mapped for retro_hsap_1259 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_33285	1487 libraries	327 libraries	13 libraries	1 library	1 library

The graphical summary, for retro_hsap_1259 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_1259 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_1259 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 31 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000049449	2 retrocopies	retro_hsap_1259 , retro_hsap_3629,
Pongo abelii	ENSPPYG00000003385	1 retrocopy	retro_pabe_2976,
Rattus norvegicus	ENSRNOG00000013452	28 retrocopies	retro_rnor_1207, retro_rnor_1224, retro_rnor_2111, retro_rnor_2112, retro_rnor_2113, retro_rnor_2352, retro_rnor_2353, retro_rnor_2354, retro_rnor_2355, retro_rnor_2408, retro_rnor_2409, retro_rnor_2410, retro_rnor_2434, retro_rnor_2435, retro_rnor_2436, retro_rnor_2437, retro_rnor_2438, retro_rnor_2486, retro_rnor_2508, retro_rnor_2509, retro_rnor_2510, retro_rnor_2511, retro_rnor_2513, retro_rnor_2664, retro_rnor_2711, retro_rnor_2716, retro_rnor_2760, retro_rnor_797,