RetrogeneDB ID: retro_hsap_2941

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 4:68904261..68905365(+)
• Located in intron of: ENSG00000248049

Retrocopy information

• Ensembl ID: ENSG00000227725
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: POLR2M
• Ensembl ID: ENSG00000255529
• Aliases: POLR2M, GCOM1, GRINL1A, Gdown, Gdown1
• Description: polymerase (RNA) II (DNA directed) polypeptide M [Source:HGNC Symbol;Acc:14862]

Sequence

>retro_hsap_2941
ATGTGCTTGCTGCCCCGCGGCTTCGAGCCCCAAGCTCCCGAGGACTTGGCGCAGCGGAGTTTGGTGGAGCTGCGGGAAAT
GTTGAAGCTCCAGGAGAGACTTTTGCGCAACGAAAAATTCATTTGCAAATTGCCCGACAAAGGTAAAAAGATCTTTGACT
CTTTTGCCAAACTGAAAGCCGCCATTGCAGAATGTGAAGAAGTTAGAAGAAAAAATGAACTGTTTCACCCTGTTAGTTTA
GACTGTAAGCTAAGGCAAAAAGCAATTGCAGAAGTTGATGTGGGTACAGATAAGGCCCGGAATTCTGACCCGATACTTGA
TACTTCATCACTAGTTCCTGGATGTTCCTCTGTAGATAACATCAAGTCATCTCAAACCTCACAAAACCAGGGACTTGGAC
GTCCTACTCTTGAAGGTGATGAAGAGACTTCAGAGGTTGAGTACACAGTGAATAAGGGCCCAGCTTCCAGCAACAGAGAC
AGGGTACCACCTTCATCTGAAGCTAGTGAGCATCACCCGCAGCATCGTGTTTCAAGTCAGGCAGAAGATACTTCCAGCAG
CTTTGACAACCTTTTTATTGACAGGTTACAGAGGATCACCATTGCGGACCAAGGTGAACAACAGTCAGAAGAAAACGCAA
GTACTAAGAACTTGACAGGCCTTTCTAGTGGGACTCAGAAGAAACCTCATTATATGGAAGTGCTAGAAATGCGAGCCAAA
AACCCAGGGCCCCAGCTGCGTAAATTTAAAACCAATGTGTTACCTTTTCGACAAAATGATTCATCTAGTCATTGCCAGAA
GAGTGGGTCTCCTATTTCCTCAAAAGAGCGGCGGCGCAGGGATAAGCAGCATCTTGATGACATCACAGCAGCTCGGCTTC
TACCACTTCACCATATGCCCACGCAGCTGCTCTCCATAGAAGAATCCTTGGCACTTCAGAAACAGCAGAAACAGAATTAT
GAGGAGATGCAAGCAAAGCTCGCAGCGCAAAAATTAGCTGAAAGACCGAATATTAAAATGCGGAGTTATAATCCAGAAGG
GGAGTCTTCAGGGAGATACCGAGAAGTAAGGGATGAAGATGACGATTGGTCCTCTGATGAATTC

Alignment

ORF - retro_hsap_2941 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.28 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MCSLPRGFEPQAPEDLAQRSLVELREMLKRQERLLRNEKFICKLPDKGKKIFDSFAKLKAAIAECEEVRR
          MC.LPRGFEPQAPEDLAQRSLVELREMLK.QERLLRNEKFICKLPDKGKKIFDSFAKLKAAIAECEEVRR
Retrocopy MCLLPRGFEPQAPEDLAQRSLVELREMLKLQERLLRNEKFICKLPDKGKKIFDSFAKLKAAIAECEEVRR

Parental  KSELFNPVSLDCKLRQKAIAEVDVGTDKAQNSDPILDTSSLVPGCSSVDNIKSSQTSQNQGLGRPTLEGD
          K.ELF.PVSLDCKLRQKAIAEVDVGTDKA.NSDPILDTSSLVPGCSSVDNIKSSQTSQNQGLGRPTLEGD
Retrocopy KNELFHPVSLDCKLRQKAIAEVDVGTDKARNSDPILDTSSLVPGCSSVDNIKSSQTSQNQGLGRPTLEGD

Parental  EETSEVEYTVNKGPASSNRDRVPPSSEASEHHPRHRVSSQAEDTSSSFDNLFIDRLQRITIADQGEQQSE
          EETSEVEYTVNKGPASSNRDRVPPSSEASEHHP.HRVSSQAEDTSSSFDNLFIDRLQRITIADQGEQQSE
Retrocopy EETSEVEYTVNKGPASSNRDRVPPSSEASEHHPQHRVSSQAEDTSSSFDNLFIDRLQRITIADQGEQQSE

Parental  ENASTKNLTGLSSGTEKKPHYMEVLEMRAKNPVPQLRKFKTNVLPFRQNDSSSHCQKSGSPISSEERRRR
          ENASTKNLTGLSSGT.KKPHYMEVLEMRAKNP.PQLRKFKTNVLPFRQNDSSSHCQKSGSPISS.ERRRR
Retrocopy ENASTKNLTGLSSGTQKKPHYMEVLEMRAKNPGPQLRKFKTNVLPFRQNDSSSHCQKSGSPISSKERRRR

Parental  DKQHLDDITAARLLPLHHMPTQLLSIEESLALQKQQKQNYEEMQAKLAAQKLAERLNIKMRSYNPEGESS
          DKQHLDDITAARLLPLHHMPTQLLSIEESLALQKQQKQNYEEMQAKLAAQKLAER.NIKMRSYNPEGESS
Retrocopy DKQHLDDITAARLLPLHHMPTQLLSIEESLALQKQQKQNYEEMQAKLAAQKLAERPNIKMRSYNPEGESS

Parental  GRYREVRDEDDDWSSDEF
          GRYREVRDEDDDWSSDEF
Retrocopy GRYREVRDEDDDWSSDEF

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	50.93 RPM
bodymap2_adrenal	0.00 RPM	57.07 RPM
bodymap2_brain	0.07 RPM	53.23 RPM
bodymap2_breast	0.14 RPM	50.06 RPM
bodymap2_colon	0.02 RPM	56.83 RPM
bodymap2_heart	0.00 RPM	35.87 RPM
bodymap2_kidney	0.27 RPM	45.79 RPM
bodymap2_liver	0.00 RPM	11.60 RPM
bodymap2_lung	0.28 RPM	62.69 RPM
bodymap2_lymph_node	0.00 RPM	59.33 RPM
bodymap2_ovary	0.04 RPM	75.04 RPM
bodymap2_prostate	0.10 RPM	68.09 RPM
bodymap2_skeletal_muscle	0.25 RPM	29.97 RPM
bodymap2_testis	0.62 RPM	63.31 RPM
bodymap2_thyroid	0.02 RPM	73.80 RPM
bodymap2_white_blood_cells	0.10 RPM	47.21 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_2941 was not detected

EST

No EST(s) were mapped for retro_hsap_2941 retrocopy.

TSS

No TSS is located nearby retro_hsap_2941 retrocopy 5' end.

Lab

retro_hsap_2941 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_2941 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000255529	1 retrocopy	retro_hsap_2941 ,
Sus scrofa	ENSSSCG00000030605	1 retrocopy	retro_sscr_547,
Ictidomys tridecemlineatus	ENSSTOG00000026874	1 retrocopy	retro_itri_80,