RetrogeneDB ID: retro_hsap_1197

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 13:46844211..46844754(+)
• Located in intron of: ENSG00000173988

Retrocopy information

• Ensembl ID: ENSG00000251106
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: FAM206A
• Ensembl ID: ENSG00000119328
• Aliases: FAM206A, C9orf6, CG-8
• Description: family with sequence similarity 206, member A [Source:HGNC Symbol;Acc:1364]

Sequence

>retro_hsap_1197
ATGGCTACCGAGCGCCAAACCGCAGAGCCGGTGGTGCCTTTGTTCGTGGATCAATACTTCACTCGCTGGTACAAAGCAGA
TGTCAAAGGAAGATCTTGTAAGGACCACTGTATACCACAGCACTCTAACCGAATATGTGTCATCACATTGGCAGAATCTC
ATCCAGTTCTTCAGAGTGGAAAAACAATTAAAAGCATTCCCTGTCAGATCAGTCCCAACTGTAGCAGACTTCAGAACAAG
GTCTCTGGGAAATTTAAGTGGGGGGCACAGTTTCTAACAGAACTTGCACCTCTCTGTAAGATTTACTGCTCAGATGGCGA
AGAATATACTGTATCTAGTTGTGTTAGAGGATGTTCGATGGAAGTGAATGAAAAACATTCTCCATAAGCCATCTATTCTT
CAAGAAAAGCCATCACTGAAGGCTACATTGCAGTTGAGTTACCCAAATTTGAAGAAAGTAAAAACATAACAGAAGGGTTA
CTGACACAAAAACGGTATGAAGAAGTCATGGTGAAATGCATTAATGCCACAACAGTGACGTCA

Alignment

ORF - retro_hsap_1197 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.89 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MATEPEAAEPVVPSLVDRYFTRWYKPDVKGKFCEDHCILQHSNRICVITLAESHPVLQSGKTIKSISYQI
          MATE...AEPVVP..VD.YFTRWYK.DVKG..C.DHCI.QHSNRICVITLAESHPVLQSGKTIKSI..QI
Retrocopy MATERQTAEPVVPLFVDQYFTRWYKADVKGRSCKDHCIPQHSNRICVITLAESHPVLQSGKTIKSIPCQI

Parental  STNCSRLQNKVSGKFKRGAQFLTELAPLCKIYCSDGEEYTVSSCVRGRLMEVNE-NILHKPSILQEKPS-
          S.NCSRLQNKVSGKFK.GAQFLTELAPLCKIYCSDGEEYTVSSCVRG..MEVNE.NILHKPSILQEKPS.
Retrocopy SPNCSRLQNKVSGKFKWGAQFLTELAPLCKIYCSDGEEYTVSSCVRGCSMEVNE>NILHKPSILQEKPS<

Parental  TEGYIAVVLPKFEESKSITEGLLTQKQYEEVMVKRINATTATS
          TEGYIAV.LPKFEESK.ITEGLLTQK.YEEVMVK.INATT.TS
Retrocopy TEGYIAVELPKFEESKNITEGLLTQKRYEEVMVKCINATTVTS

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	13.06 RPM
bodymap2_adrenal	0.00 RPM	14.08 RPM
bodymap2_brain	0.00 RPM	12.80 RPM
bodymap2_breast	0.00 RPM	18.17 RPM
bodymap2_colon	0.00 RPM	20.15 RPM
bodymap2_heart	0.00 RPM	13.24 RPM
bodymap2_kidney	0.00 RPM	19.30 RPM
bodymap2_liver	0.00 RPM	8.94 RPM
bodymap2_lung	0.00 RPM	10.94 RPM
bodymap2_lymph_node	0.00 RPM	10.11 RPM
bodymap2_ovary	0.00 RPM	20.38 RPM
bodymap2_prostate	0.00 RPM	22.71 RPM
bodymap2_skeletal_muscle	0.00 RPM	11.39 RPM
bodymap2_testis	0.00 RPM	28.20 RPM
bodymap2_thyroid	0.00 RPM	20.06 RPM
bodymap2_white_blood_cells	0.00 RPM	20.02 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_1197 was not detected

EST

No EST(s) were mapped for retro_hsap_1197 retrocopy.

TSS

No TSS is located nearby retro_hsap_1197 retrocopy 5' end.

Lab

retro_hsap_1197 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_1197 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_997

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004996	1 retrocopy	retro_btau_873,
Canis familiaris	ENSCAFG00000028510	1 retrocopy	retro_cfam_1345,
Cavia porcellus	ENSCPOG00000005927	1 retrocopy	retro_cpor_1488,
Dipodomys ordii	ENSDORG00000008618	1 retrocopy	retro_dord_611,
Homo sapiens	ENSG00000119328	1 retrocopy	retro_hsap_1197 ,
Macropus eugenii	ENSMEUG00000013637	1 retrocopy	retro_meug_1321,
Microcebus murinus	ENSMICG00000002074	1 retrocopy	retro_mmur_1363,
Monodelphis domestica	ENSMODG00000012563	1 retrocopy