RetrogeneDB ID: retro_hsap_35

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 9:71395080..71395944(+)
• Located in intron of: ENSG00000107242

Retrocopy information

• Ensembl ID: ENSG00000187866
• Aliases: FAM122A, C9orf42
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: FAM122C
• Ensembl ID: ENSG00000156500
• Aliases: None
• Description: family with sequence similarity 122C [Source:HGNC Symbol;Acc:25202]

Sequence

>retro_hsap_35
ATGGCTCAGGAGAAGATGGAGCTAGACCTGGAGCTGCCTCCGGGTACGGGCGGGAGCCCGGCGGAGGGCGGTGGCAGCGG
CGGCGGCGGGGGCCTCAGGAGGTCTAACAGCGCCCCCCTGATCCACGGCCTCAGTGACACTTCGCCGGTGTTCCAGGCCG
AGGCGCCGAGCGCCAGGCGGAACAGCACAACGTTCCCGAGCCGCCACGGCCTGCTGCTGCCGGCCTCCCCTGTCCGCATG
CACAGCAGCCGCTTGCACCAGATCAAACAAGAAGAGGGCATGGACTTGATCAACCGAGAGACGGTCCACGAACGGGAGGT
GCAGACCGCAATGCAGATAAGCCACTCCTGGGAGGAAAGTTTCAGCCTGAGTGACAACGACGTGGAGAAATCCGCCTCCC
CCAAGCGCATCGATTTCATTCCTGTGTCACCAGCACCGTCACCCACTCGGGGAATTGGGAAGCAGTGTTTTTCGCCATCC
TTGCAAAGTTTTGTAAGTAGCAACGGATTGCCTCCAAGCCCTATTCCCAGCCCAACGACCCGATTTACCACCCGGAGAAG
CCAGAGCCCCATCAATTGCATTAGACCAAGTGTTCTTGGACCATTGAAAAGAAAATGTGAAATGGAAACTGAATATCAGC
CAAAGAGATTTTTCCAGGGCATCACCAACATGCTTTCTTCTGACGTTGCACAGCTGTCAGATCCTGGTGTGTGTGTATCT
TCGGATACCCTTGATGGAAACAGCAGCAGTGCCGGATCTTCTTGTAACTCACCAGCGAAAGTCAGCACTACCACCGACTC
TCCTGTGTCACCTGCCCAAGCGGCTTCTCCATTTATTCCACTAGATGAACTTTCGTCTAAGTGA

Alignment

ORF - retro_hsap_35 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.47 %
• Parental protein coverage: 98.38 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDLINRETMSEWKLQSEIQISHSWEEGLKLNDNGLQKSSSLKCIDLTPVSSMASSIKKTGKQCFSPSLQT
          MDLINRET..E...Q...QISHSWEE...L.DN...KS.S.K.ID..PVS...S.....GKQCFSPSLQ.
Retrocopy MDLINRETVHEREVQTAMQISHSWEESFSLSDNDVEKSASPKRIDFIPVSPAPSPTRGIGKQCFSPSLQS

Parental  CVSCTGSPSSPIPSPMQQYIIR-SQNPTNIIRPSILGPLKRKGEMAFQYQPKKIFQGTTNMLSSDTSQLS
          .VS..G.P.SPIPSP......R.SQ.P.N.IRPS.LGPLKRK.EM...YQPK..FQG.TNMLSSD..QLS
Retrocopy FVSSNGLPPSPIPSPTTRFTTRRSQSPINCIRPSVLGPLKRKCEMETEYQPKRFFQGITNMLSSDVAQLS

Parental  ENNVYLLPATFDGNDSNAGSSGNSSAEIGTVTNSPVSPSDTGS
          ...V.....T.DGN.S.AGSS.NS.A...T.T.SPVSP....S
Retrocopy DPGVCVSSDTLDGNSSSAGSSCNSPAKVSTTTDSPVSPAQAAS

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	9.20 RPM	4.11 RPM
bodymap2_adrenal	9.25 RPM	5.12 RPM
bodymap2_brain	8.58 RPM	3.49 RPM
bodymap2_breast	8.31 RPM	3.23 RPM
bodymap2_colon	10.71 RPM	2.22 RPM
bodymap2_heart	8.55 RPM	1.81 RPM
bodymap2_kidney	5.98 RPM	1.78 RPM
bodymap2_liver	3.30 RPM	0.13 RPM
bodymap2_lung	3.22 RPM	7.35 RPM
bodymap2_lymph_node	7.18 RPM	2.14 RPM
bodymap2_ovary	8.98 RPM	11.51 RPM
bodymap2_prostate	9.91 RPM	4.35 RPM
bodymap2_skeletal_muscle	9.95 RPM	0.67 RPM
bodymap2_testis	9.94 RPM	8.96 RPM
bodymap2_thyroid	10.87 RPM	3.39 RPM
bodymap2_white_blood_cells	12.62 RPM	3.05 RPM

ChIP-Seq

RNA Polymerase II activity may be related with retro_hsap_35 in 50 libraries

ENCODE library ID	Target	ChIP-Seq Peak coordinates
ENCFF002CFW	POLR2A	9:71394695..71395189
ENCFF002CFX	POLR2A	9:71394696..71395174
ENCFF002CGN	POLR2A	9:71394786..71395138
ENCFF002CHO	POLR2A	9:71394390..71395492
ENCFF002CIH	POLR2A	9:71394615..71394928
ENCFF002CIO	POLR2A	9:71394598..71395161
ENCFF002CJE	POLR2A	9:71394593..71395026
ENCFF002CJZ	POLR2A	9:71394624..71395153
ENCFF002CKX	POLR2A	9:71394647..71395179
ENCFF002CLM	POLR2A	9:71394656..71395196
ENCFF002CMI	POLR2A	9:71394416..71395230
ENCFF002COJ	POLR2A	9:71394785..71395221
ENCFF002CPG	POLR2A	9:71394704..71394922
ENCFF002CPG	POLR2A	9:71394761..71395251
ENCFF002CPH	POLR2A	9:71394602..71394992
ENCFF002CQA	POLR2A	9:71394616..71394908
ENCFF002CQA	POLR2A	9:71394705..71395275
ENCFF002CQC	POLR2A	9:71394674..71395144
ENCFF002CQE	POLR2A	9:71394664..71395159
ENCFF002CQG	POLR2A	9:71394895..71395126
ENCFF002CQI	POLR2A	9:71394722..71395181
ENCFF002CQK	POLR2A	9:71394646..71395226
ENCFF002CQM	POLR2A	9:71394672..71395152
ENCFF002CQO	POLR2A	9:71394629..71395178
ENCFF002CRK	POLR2A	9:71394693..71395217
ENCFF002CRO	POLR2A	9:71394588..71395008
ENCFF002CSY	POLR2A	9:71394580..71395168
ENCFF002CUP	POLR2A	9:71394806..71394903
ENCFF002CUQ	POLR2A	9:71394653..71394936
ENCFF002CVF	POLR2A	9:71394605..71395021
ENCFF002CVJ	POLR2A	9:71394667..71394898
ENCFF002CXM	POLR2A	9:71394564..71395054
ENCFF002CXN	POLR2A	9:71394568..71395064
ENCFF002CXO	POLR2A	9:71394580..71395004
ENCFF002CXP	POLR2A	9:71394593..71395073
ENCFF002CXP	POLR2A	9:71394792..71395272
ENCFF002CXR	POLR2A	9:71394718..71395083
ENCFF002CZC	POLR2A	9:71394606..71395109
ENCFF002CZD	POLR2A	9:71394634..71395110
ENCFF002CZQ	POLR2A	9:71394726..71395011
ENCFF002CZW	POLR2A	9:71394523..71395290
ENCFF002CZY	POLR2A	9:71394588..71395196
ENCFF002DAE	POLR2A	9:71394714..71395024
ENCFF002DAH	POLR2A	9:71394931..71395044
ENCFF002DAK	POLR2A	9:71394571..71395071
ENCFF002DAS	POLR2A	9:71394588..71395064
ENCFF002DAV	POLR2A	9:71394633..71395177
ENCFF002DBB	POLR2A	9:71394913..71395113
ENCFF002DBE	POLR2A	9:71394601..71395097
ENCFF002DBO	POLR2A	9:71394883..71395137
ENCFF002DBP	POLR2A	9:71394951..71395111
ENCFF002DBQ	POLR2A	9:71394658..71395028
ENCFF002DBT	POLR2A	9:71394648..71395018
ENCFF002DBT	POLR2A	9:71394847..71395217

EST

4 EST(s) were mapped to retro_hsap_35 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
AW798921	71395666	71395814	100	148	0	148
BF926702	71395208	71395606	98	390	7	381
BM720476	71395636	71395769	100	133	0	133
HY293038	71395072	71395539	99.8	466	1	465

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_193686	19 libraries	0 libraries	17 libraries	196 libraries	1597 libraries
TSS #2	TSS_193687	1498 libraries	294 libraries	37 libraries	0 libraries	0 libraries

The graphical summary, for retro_hsap_35 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_35 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_35 has 6 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Mus musculus	retro_mmus_22
Rattus norvegicus	retro_rnor_651
Oryctolagus cuniculus	retro_ocun_205
Bos taurus	retro_btau_103
Canis familiaris	retro_cfam_181
Equus caballus	retro_ecab_91

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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	ENSG00000156500	1 retrocopy	retro_hsap_35 ,
Nomascus leucogenys	ENSNLEG00000002084	1 retrocopy	retro_nleu_2475,
Oryctolagus cuniculus	ENSOCUG00000029737	1 retrocopy	retro_ocun_205,