RetrogeneDB ID: retro_hsap_37

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 1:12907260..12908142(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000179172
• Aliases: HNRNPCL1, HNRPCL1
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: RALY
• Ensembl ID: ENSG00000125970
• Aliases: RALY, HNRPCL2, P542
• Description: RNA binding protein, autoantigenic (hnRNP-associated with lethal yellow homolog (mouse)) [Source:HGNC Symbol;Acc:15921]

Sequence

>retro_hsap_37
ATGGCCAGCAACGTTACCAACAAGATGGATCCTCACTCCATGAACTCCCGTGTGTTCATTGGGAATCTCAACACTCTTGT
TGTCAAGAAATCGGATGTGGAGGCGATCTTTTCCAAGTATGGCAAAATTGCGGGCTGCTCTGTTCATAAGGGCTTTGCCT
TCGTTCAATATGATAAGGAGAAAAATGCCCGGGCTGCTGTAGCAGGAGAGGATGGCAGAATGATTGCTAGCCAGGTTGTA
GATATTAACCTGGCTGCAGAGCCAAAAGTGAACCGAGGAAACGCAGGTGTGAAACGATCAGCAGCGGAGATGTACGGCTC
CTCTTTTGACTTGGACTATGGCTTTCAACGGGATTATTATGATGGAATGTACAGTTTCCCAGCACGTGTACCTCCTCCTC
CTCCCATTGCTCTGGCTGTAGTGCCCTCGAAACGTCAACGTCTATCAGGAAACACCTCACGAAGGGGCAAAAGTGGCTTC
AATTCTAAGAGTGGAAAGCGGGGATCTTCCAAGTCTGGAAAGTTGAAAGGTGATGACCTTCAGGCCATTAAGCAGGAGTT
GACCCAGATAAAACAGAAAGTGGATTCTCTCCTGGAAAACCTGGAAAAAATTGAAAAGGAACAGAGCAAACAAGAGGTAG
AGGTGAAAAATGCTAAGTCAGAAGAGGAGCAGAGCAGTAGCTCCATGAAGAAAGATGAGACTCATGTGAAGATGGAGTCT
GAGGGGGGTGCAGAAGACTCTGCTGAGGAGGGGGACCCACTGGATGATGATGTTAATGAAGATCAGGGGGATGACCAGCT
GGAGTTGATCAAGGATGATGAAAAAGAGGCTGAGGAAGGAGAGGATGACAGAGACAGCACCAATGGCCAGGATGACTCTT
AA

Alignment

ORF - retro_hsap_37 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.99 %
• Parental protein coverage: 68.3 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ASNVTNKNDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVHKGYAFVQYSNERHARAAVLGEN
          ASNVTNK.DP.S.NSRVFIGNLNT..VKKSDVE.IFSKYG..AGCSVHKG.AFVQY..E..ARAAV.GE.
Retrocopy ASNVTNKMDPHSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIAGCSVHKGFAFVQYDKEKNARAAVAGED

Parental  GRVLAGQTLDINMAGEPKPDRPK-GLKRAASAIYSGYIFDYDY-YRDDFYDRLFDYRGRLSPVP--VPRA
          GR..A.Q..DIN.A.EPK..R...G.KR.A...Y.G..FD.DY....D.YD.......R..P.P......
Retrocopy GRMIASQVVDINLAAEPKVNRGNAGVKRSAAEMY-GSSFDLDYGFQRDYYDGMYSFPARVPPPPPIALAV

Parental  VPVKRPRVTVPLVRRVKTNVPVKLFARSTAVTTSSAKIKLKSSELQAIKTELTQIKSNIDALLSRLEQIA
          VP.KR.R......RR.K.....K...R.......S.K.K.....LQAIK.ELTQIK...D.LL..LE.I.
Retrocopy VPSKRQRLSGNTSRRGKSGFNSKSGKRG---SSKSGKLK--GDDLQAIKQELTQIKQKVDSLLENLEKIE

Parental  AEQ
          .EQ
Retrocopy KEQ

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	0.02 RPM	59.93 RPM
bodymap2_adrenal	0.04 RPM	66.77 RPM
bodymap2_brain	0.00 RPM	24.19 RPM
bodymap2_breast	0.00 RPM	40.10 RPM
bodymap2_colon	0.00 RPM	51.28 RPM
bodymap2_heart	0.00 RPM	29.39 RPM
bodymap2_kidney	0.00 RPM	47.09 RPM
bodymap2_liver	0.00 RPM	19.56 RPM
bodymap2_lung	0.00 RPM	82.95 RPM
bodymap2_lymph_node	0.00 RPM	66.97 RPM
bodymap2_ovary	0.08 RPM	49.29 RPM
bodymap2_prostate	0.00 RPM	65.78 RPM
bodymap2_skeletal_muscle	0.00 RPM	51.33 RPM
bodymap2_testis	0.06 RPM	76.83 RPM
bodymap2_thyroid	0.04 RPM	66.42 RPM
bodymap2_white_blood_cells	0.00 RPM	91.51 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_37 was not detected

EST

No EST(s) were mapped for retro_hsap_37 retrocopy.

TSS

No TSS is located nearby retro_hsap_37 retrocopy 5' end.

Lab

retro_hsap_37 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_37 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000092199	2 retrocopies	retro_hsap_1624, retro_hsap_3740,
Homo sapiens	ENSG00000125970	1 retrocopy	retro_hsap_37 ,