RetrogeneDB ID: retro_hsap_12

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 14:61746809..61747865(-)
• Located in intron of: ENSG00000027075

Retrocopy information

• Ensembl ID: ENSG00000182107
• Aliases: TMEM30B, CDC50B
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: TMEM30A
• Ensembl ID: ENSG00000112697
• Aliases: TMEM30A, C6orf67, CDC50A
• Description: transmembrane protein 30A [Source:HGNC Symbol;Acc:16667]

Sequence

>retro_hsap_12
ATGACCTGGAGCGCCACGGCCCGGGGCGCCCACCAGCCCGACAACACCGCCTTCACTCAGCAGCGCCTCCCCGCCTGGCA
GCCGCTGCTGTCGGCCAGCATCGCGCTGCCGCTCTTCTTCTGCGCGGGCCTGGCCTTCATCGGCCTGGGCCTGGGCCTCT
ACTACTCCTCCAACGGCATCAAGGAGCTGGAGTACGACTATACAGGCGACCCGGGCACCGGTAACTGCTCGGTGTGCGCC
GCGGCTGGCCAGGGCCGGGCGCTGCCGCCCCCCTGCTCGTGCGCCTGGTACTTCTCGCTGCCCGAGCTCTTCCAGGGCCC
AGTGTACCTCTACTACGAGCTGACCAACTTCTACCAGAACAACCGGCGCTACGGCGTGTCCCGCGACGACGCGCAGCTGA
GCGGACTCCCCAGCGCGCTGCGCCACCCTGTCAACGAGTGCGCCCCCTACCAGCGCAGCGCGGCCGGCCTGCCCATCGCG
CCCTGCGGCGCCATCGCCAACAGCCTCTTCAACGACTCCTTCTCGCTTTGGCACCAGCGCCAGCCCGGCGGGCCCTACGT
CGAGGTGCCGCTCGACCGCTCCGGCATCGCCTGGTGGACCGACTACCACGTCAAGTTCCGCAACCCGCCGCTGGTCAACG
GCAGCCTGGCGTTGGCCTTCCAGGGCACGGCGCCCCCGCCCAACTGGCGCCGGCCAGTCTACGAGCTCAGCCCCGACCCC
AACAACACCGGCTTCATCAATCAGGACTTCGTGGTGTGGATGCGCACGGCGGCGCTGCCCACGTTCCGCAAACTGTACGC
GCGCATCCGCCAGGGCAACTACTCGGCCGGGCTGCCGCGGGGCGCCTACCGCGTCAACATCACCTACAACTACCCGGTGC
GCGCGTTCGGCGGCCACAAGCTCCTCATCTTCAGCAGCATCTCGTGGATGGGTGGCAAGAACCCCTTCCTGGGCATCGCC
TACCTGGTCGTCGGCTCCCTCTGCATCCTCACCGGCTTTGTCATGCTGGTCGTCTACATTCGCTACCAGGACCAGGACGA
CGACGACGAGGAGTGA

Alignment

ORF - retro_hsap_12 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.43 %
• Parental protein coverage: 70.64 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PCFCTINFTLEKSFEGNVFMYYGLSNFYQNHRRYVKSRDDSQLNGDSSALLNPSKECEPYRRNE-DKPIA
          PC.C...F.L...F.G.V..YY.L.NFYQN.RRY..SRDD.QL.G..SAL..P..EC.PY.R.....PIA
Retrocopy PCSCAWYFSLPELFQGPVYLYYELTNFYQNNRRYGVSRDDAQLSGLPSALRHPVNECAPYQRSAAGLPIA

Parental  PCGAIANSMFNDTLELFLIGNDSYP-IPIALKKKGIAWWTDKNVKFRNPP-GGDNLEERFKGTTKPVNWL
          PCGAIANS.FND...L........P.....L...GIAWWTD..VKFRNPP.....L...F.GT..P.NW.
Retrocopy PCGAIANSLFNDSFSLWHQRQPGGPYVEVPLDRSGIAWWTDYHVKFRNPPLVNGSLALAFQGTAPPPNWR

Parental  KPVYMLDSDPDNNGFINEDFIVWMRTAALPTFRKLYRLIERKSDLHPTLPAGRYSLNVTYNYPVHYFDGR
          .PVY.L..DP.N.GFIN.DF.VWMRTAALPTFRKLY..I.R.......LP.G.Y..N.TYNYPV..F.G.
Retrocopy RPVYELSPDPNNTGFINQDFVVWMRTAALPTFRKLYARI-RQGNYSAGLPRGAYRVNITYNYPVRAFGGH

Parental  KRMILSTISWMGGKNPFLGIAYIAVGSISFLLGVVLLVINHKYRNSSN
          K..I.S.ISWMGGKNPFLGIAY..VGS...L.G.V.LV....Y.....
Retrocopy KLLIFSSISWMGGKNPFLGIAYLVVGSLCILTGFVMLVVYIRYQDQDD

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	0.99 RPM	263.12 RPM
bodymap2_adrenal	0.80 RPM	269.64 RPM
bodymap2_brain	0.09 RPM	478.86 RPM
bodymap2_breast	1.23 RPM	232.10 RPM
bodymap2_colon	1.30 RPM	302.78 RPM
bodymap2_heart	0.04 RPM	108.11 RPM
bodymap2_kidney	3.43 RPM	286.07 RPM
bodymap2_liver	0.78 RPM	131.24 RPM
bodymap2_lung	4.10 RPM	400.02 RPM
bodymap2_lymph_node	1.21 RPM	214.39 RPM
bodymap2_ovary	0.79 RPM	204.28 RPM
bodymap2_prostate	5.01 RPM	254.52 RPM
bodymap2_skeletal_muscle	0.56 RPM	82.70 RPM
bodymap2_testis	2.66 RPM	220.58 RPM
bodymap2_thyroid	18.25 RPM	340.26 RPM
bodymap2_white_blood_cells	0.63 RPM	302.19 RPM

ChIP-Seq

RNA Polymerase II activity may be related with retro_hsap_12 in 8 libraries

ENCODE library ID	Target	ChIP-Seq Peak coordinates
ENCFF002CFW	POLR2A	14:61747330..61747650
ENCFF002CFX	POLR2A	14:61747319..61747623
ENCFF002CJE	POLR2A	14:61747645..61748281
ENCFF002CJE	POLR2A	14:61747846..61748482
ENCFF002DAE	POLR2A	14:61747335..61747645
ENCFF002DBB	POLR2A	14:61747391..61747591
ENCFF002DBO	POLR2A	14:61747103..61747652
ENCFF002DBO	POLR2A	14:61747714..61748453
ENCFF002DBP	POLR2A	14:61747900..61748174
ENCFF002DBP	POLR2A	14:61748218..61748457
ENCFF002DBQ	POLR2A	14:61748261..61748457
ENCFF002DBQ	POLR2A	14:61747901..61748271

EST

1 EST(s) were mapped to retro_hsap_12 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
DB209474	61746771	61747310	99.7	537	2	535

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_39245	1449 libraries	234 libraries	125 libraries	21 libraries	0 libraries
TSS #2	TSS_39246	1585 libraries	219 libraries	25 libraries	0 libraries	0 libraries
TSS #3	TSS_39247	1419 libraries	284 libraries	126 libraries	0 libraries	0 libraries
TSS #4	TSS_39248	1328 libraries	168 libraries	96 libraries	66 libraries	171 libraries
TSS #5	TSS_39249	1481 libraries	147 libraries	178 libraries	20 libraries	3 libraries
TSS #6	TSS_39250	1564 libraries	175 libraries	87 libraries	3 libraries	0 libraries
TSS #7	TSS_39251	1303 libraries	153 libraries	114 libraries	54 libraries	205 libraries
TSS #8	TSS_39252	1373 libraries	156 libraries	146 libraries	123 libraries	31 libraries
TSS #9	TSS_39253	1493 libraries	150 libraries	180 libraries	6 libraries	0 libraries
TSS #10	TSS_39254	1416 libraries	135 libraries	241 libraries	28 libraries	9 libraries
TSS #11	TSS_39255	1417 libraries	190 libraries	209 libraries	9 libraries	4 libraries
TSS #12	TSS_39256	1641 libraries	165 libraries	23 libraries	0 libraries	0 libraries

The graphical summary, for retro_hsap_12 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_12 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_12 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005100	1 retrocopy	retro_btau_72,
Canis familiaris	ENSCAFG00000002708	1 retrocopy	retro_cfam_26,
Callithrix jacchus	ENSCJAG00000010325	1 retrocopy	retro_cjac_801,
Cavia porcellus	ENSCPOG00000020712	1 retrocopy	retro_cpor_23,
Homo sapiens	ENSG00000112697	1 retrocopy	retro_hsap_12 ,
Myotis lucifugus	ENSMLUG00000011923	1 retrocopy	retro_mluc_1871,
Monodelphis domestica	ENSMODG00000018502	1 retrocopy	retro_mdom_287,
Mus musculus	ENSMUSG00000032328	1 retrocopy	retro_mmus_108,
Nomascus leucogenys	ENSNLEG00000004962	1 retrocopy	retro_nleu_69,
Otolemur garnettii	ENSOGAG00000015718	1 retrocopy	retro_ogar_22,
Pongo abelii	ENSPPYG00000016782	1 retrocopy	retro_pabe_204,
Pelodiscus sinensis	ENSPSIG00000007174	1 retrocopy	retro_psin_61,
Rattus norvegicus	ENSRNOG00000010895	1 retrocopy	retro_rnor_399,
Ictidomys tridecemlineatus	ENSSTOG00000002543	1 retrocopy	retro_itri_50,
Tarsius syrichta	ENSTSYG00000008211	1 retrocopy	retro_tsyr_928,