RetrogeneDB ID: retro_hsap_104

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 2:120979499..120980552(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000226479
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: TMEM185A
• Ensembl ID: ENSG00000155984
• Aliases: TMEM185A, CXorf13, FAM11A, FRAXF, ee3
• Description: transmembrane protein 185A [Source:HGNC Symbol;Acc:17125]

Sequence

>retro_hsap_104
ATGAACCCCAGGGGCCTGTTCCAGGACTTCAACCCCAGTAAGTTTCTCATCTACACCTGCCTGCTGCTCTTCTCGGTGCT
GCTGCCCCTCCGCCTGGACGGCATCATCCAATGGAGCTACTGGGCCGTCTTTGCCCCCATATGGCTGTGGAAGCTTCTAG
TCGTCGCAGGCGCCTCCGTGGGCGCGGGCGTTTGGGCCCGCAACCCTCGCTACCGCACCGAGGGAGAGGCCTGTGTGGAG
TTCAAAGCCATGCTGATCGCTGTGGGCATCCACCTGCTGCTGCTCATGTTCGAAGTCCTGGTCTGCGACAGGGTGGAGAG
GGGCACCCACTTCTGGCTGCTGGTCTTCATGCCTCTCTTCTTCGTGTCCCCCGTGTCCGTGGCTGCCTGCGTCTGGGGCT
TTCGACACGATAGGTCGCTGGAGCTGGAGATCCTGTGCTCGGTCAACATCCTGCAGTTCATCTTCATCGCCCTAAAGCTG
GACAGGATTATTCACTGGCCGTGGCTGGTGGTGTTTGTGCCCCTGTGGATCCTCATGTCGTTCCTTTGCCTGGTCGTCCT
CTATTACATCGTCTGGTCCCTCCTGTTCCTGCGGTCCCTGGATGTGGTTGCCGAGCAGCGGAGAACACACGTGACCATGG
CTATCAGTTGGATAACGATTGTCGTGCCTCTGCTCACTTTTGAGGTCCTGCTGGTTCACAGATTGGATGGCCACAATACA
TTCTCCTACGTCTCCATATTTGTCCCCCTTTGGCTTTCCTTACTAACTTTAATGGCCACAACATTTAGGCGAAAGGGGGG
CAATCATTGGTGGTTTGGCATTCGCAGAGACTTCTGTCAGTTTCTGCTTGAAATTTTCCCATTTTTAAGAGAATATGGGA
ACATTTCATATGATCTCCATCACGAAGATAGTGAAGATGCTGAAGAAACATCAGTTCCAGAAGCTCCGAAAATTGCTCCA
ATATTTGGAAAGAAGGCCAGAGTAGTTATAACCCAGAGCCCTGGGAAATACGTTCCCCCCCCTCCCAAGTTAAATATTGA
TATGCCAGATTAA

Alignment

ORF - retro_hsap_104 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.57 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNLRGLFQDFNPSKFLIYACLLLFSVLLALRLDGIIQWSYWAVFAPIWLWKLMVIVGASVGTGVWARNPQ
          MN.RGLFQDFNPSKFLIY.CLLLFSVLL.LRLDGIIQWSYWAVFAPIWLWKL.V..GASVG.GVWARNP.
Retrocopy MNPRGLFQDFNPSKFLIYTCLLLFSVLLPLRLDGIIQWSYWAVFAPIWLWKLLVVAGASVGAGVWARNPR

Parental  YRAEGETCVEFKAMLIAVGIHLLLLMFEVLVCDRIERGSHFWLLVFMPLFFVSPVSVAACVWGFRHDRSL
          YR.EGE.CVEFKAMLIAVGIHLLLLMFEVLVCDR.ERG.HFWLLVFMPLFFVSPVSVAACVWGFRHDRSL
Retrocopy YRTEGEACVEFKAMLIAVGIHLLLLMFEVLVCDRVERGTHFWLLVFMPLFFVSPVSVAACVWGFRHDRSL

Parental  ELEILCSVNILQFIFIALRLDKIIHWPWLVVCVPLWILMSFLCLVVLYYIVWSVLFLRSMDVIAEQRRTH
          ELEILCSVNILQFIFIAL.LD.IIHWPWLVV.VPLWILMSFLCLVVLYYIVWS.LFLRS.DV.AEQRRTH
Retrocopy ELEILCSVNILQFIFIALKLDRIIHWPWLVVFVPLWILMSFLCLVVLYYIVWSLLFLRSLDVVAEQRRTH

Parental  ITMALSWMTIVVPLLTFEILLVHKLDGHNAFSSIPIFVPLWLSLITLMATTFGQKGGNHWWFGIRKDFCQ
          .TMA.SW.TIVVPLLTFE.LLVH.LDGHN.FS...IFVPLWLSL.TLMATTF..KGGNHWWFGIR.DFCQ
Retrocopy VTMAISWITIVVPLLTFEVLLVHRLDGHNTFSYVSIFVPLWLSLLTLMATTFRRKGGNHWWFGIRRDFCQ

Parental  FLLEIFPFLREYGNISYDLHHEDNEETEETPVPEPPKIAPMFRKKARVVITQSPGKYVLPPPKLNIEMPD
          FLLEIFPFLREYGNISYDLHHED.E..EET.VPE.PKIAP.F.KKARVVITQSPGKYV.PPPKLNI.MPD
Retrocopy FLLEIFPFLREYGNISYDLHHEDSEDAEETSVPEAPKIAPIFGKKARVVITQSPGKYVPPPPKLNIDMPD

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	8.98 RPM	5.59 RPM
bodymap2_adrenal	11.20 RPM	5.04 RPM
bodymap2_brain	5.93 RPM	4.81 RPM
bodymap2_breast	9.55 RPM	4.84 RPM
bodymap2_colon	7.08 RPM	5.39 RPM
bodymap2_heart	8.22 RPM	7.03 RPM
bodymap2_kidney	9.31 RPM	5.13 RPM
bodymap2_liver	2.66 RPM	1.31 RPM
bodymap2_lung	7.19 RPM	2.95 RPM
bodymap2_lymph_node	7.02 RPM	5.34 RPM
bodymap2_ovary	12.11 RPM	10.26 RPM
bodymap2_prostate	9.11 RPM	6.62 RPM
bodymap2_skeletal_muscle	8.77 RPM	0.91 RPM
bodymap2_testis	14.54 RPM	9.88 RPM
bodymap2_thyroid	12.69 RPM	6.89 RPM
bodymap2_white_blood_cells	11.75 RPM	4.98 RPM

ChIP-Seq

RNA Polymerase II activity may be related with retro_hsap_104 in 46 libraries

ENCODE library ID	Target	ChIP-Seq Peak coordinates
ENCFF002CFW	POLR2A	2:120980443..120981326
ENCFF002CFX	POLR2A	2:120980458..120981320
ENCFF002CGN	POLR2A	2:120980622..120981068
ENCFF002CHO	POLR2A	2:120980378..120981566
ENCFF002CIH	POLR2A	2:120980851..120980999
ENCFF002CIO	POLR2A	2:120980595..120981052
ENCFF002CJE	POLR2A	2:120980703..120981074
ENCFF002CJZ	POLR2A	2:120980716..120981098
ENCFF002CKX	POLR2A	2:120980771..120981078
ENCFF002CKX	POLR2A	2:120981051..120981202
ENCFF002CLM	POLR2A	2:120980641..120981181
ENCFF002CMI	POLR2A	2:120980500..120981342
ENCFF002COJ	POLR2A	2:120980689..120981125
ENCFF002CPG	POLR2A	2:120980647..120981137
ENCFF002CPH	POLR2A	2:120980696..120981086
ENCFF002CQA	POLR2A	2:120980592..120981162
ENCFF002CQC	POLR2A	2:120980681..120981035
ENCFF002CQC	POLR2A	2:120980871..120981351
ENCFF002CQE	POLR2A	2:120980671..120981075
ENCFF002CQE	POLR2A	2:120980994..120981252
ENCFF002CQG	POLR2A	2:120980673..120981015
ENCFF002CQI	POLR2A	2:120980708..120981059
ENCFF002CQK	POLR2A	2:120980608..120981321
ENCFF002CQM	POLR2A	2:120980660..120981058
ENCFF002CQO	POLR2A	2:120980586..120981072
ENCFF002CRK	POLR2A	2:120980908..120981432
ENCFF002CRO	POLR2A	2:120980716..120981136
ENCFF002CSY	POLR2A	2:120980641..120981163
ENCFF002CUP	POLR2A	2:120980763..120981079
ENCFF002CUQ	POLR2A	2:120980676..120981180
ENCFF002CVF	POLR2A	2:120980709..120981125
ENCFF002CVJ	POLR2A	2:120980746..120981054
ENCFF002CXM	POLR2A	2:120980643..120981133
ENCFF002CXN	POLR2A	2:120980661..120981157
ENCFF002CXO	POLR2A	2:120980678..120981102
ENCFF002CXP	POLR2A	2:120980752..120981039
ENCFF002CXR	POLR2A	2:120980704..120981014
ENCFF002CZC	POLR2A	2:120980562..120981123
ENCFF002CZD	POLR2A	2:120980584..120981321
ENCFF002DAE	POLR2A	2:120980790..120981100
ENCFF002DAE	POLR2A	2:120981036..120981346
ENCFF002DAH	POLR2A	2:120980797..120981081
ENCFF002DAK	POLR2A	2:120980597..120981097
ENCFF002DAV	POLR2A	2:120980597..120981141
ENCFF002DBB	POLR2A	2:120980834..120981034
ENCFF002DBE	POLR2A	2:120980766..120981049
ENCFF002DBO	POLR2A	2:120980625..120981079
ENCFF002DBP	POLR2A	2:120980771..120981038
ENCFF002DBQ	POLR2A	2:120980743..120981113
ENCFF002DBT	POLR2A	2:120980748..120981118

EST

5 EST(s) were mapped to retro_hsap_104 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
AA256930	120979906	120980225	100	319	0	319
BE143874	120979779	120980045	99.7	265	1	264
BF349607	120979557	120980049	95.8	470	3	454
BF800502	120979772	120980109	100	336	0	335
HY301666	120979535	120980044	100	509	0	509

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_111735	686 libraries	811 libraries	315 libraries	14 libraries	3 libraries
TSS #2	TSS_111736	114 libraries	127 libraries	1099 libraries	367 libraries	122 libraries
TSS #3	TSS_111737	499 libraries	795 libraries	527 libraries	7 libraries	1 library
TSS #4	TSS_111738	26 libraries	1 library	30 libraries	173 libraries	1599 libraries

The graphical summary, for retro_hsap_104 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

• Experiment type: PCR amplification
• Forward primer: TCGTGCCTCTGCTCACTTTT (20 nt long)
• Reverse primer: GCAAAGCCCAAGGAGAGAGT (20 nt long)
• Annealing temperature: 56 °C
• (Expected) product size: 883
• Electrophoresis gel image:
• Additional comment: Red arrow indicates PCR product of retrogene in pooled cDNA from 16 human tissues (Clontech). Red number of lane indicates particular retrogene; L - GeneRuler 100 bp DNA Ladder (Thermo Fisher Scientific); N - No template control (water instead of cDNA)

Homology

Retrocopy orthology:

Retrocopy retro_hsap_104 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_189
Pongo abelii	retro_pabe_118
Macaca mulatta	retro_mmul_310
Mus musculus	retro_mmus_358
Rattus norvegicus	retro_rnor_6

---

Parental genes homology:

Parental genes homology involve 26 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000008637	1 retrocopy	retro_acar_65,
Ailuropoda melanoleuca	ENSAMEG00000009351	1 retrocopy	retro_amel_8,
Bos taurus	ENSBTAG00000006818	1 retrocopy	retro_btau_1,
Canis familiaris	ENSCAFG00000019103	1 retrocopy	retro_cfam_159,
Cavia porcellus	ENSCPOG00000003622	1 retrocopy	retro_cpor_5,
Dasypus novemcinctus	ENSDNOG00000011864	1 retrocopy	retro_dnov_2451,
Dipodomys ordii	ENSDORG00000015027	1 retrocopy	retro_dord_67,
Equus caballus	ENSECAG00000009399	1 retrocopy	retro_ecab_426,
Felis catus	ENSFCAG00000024483	1 retrocopy	retro_fcat_1116,
Homo sapiens	ENSG00000155984	1 retrocopy	retro_hsap_104 ,
Gorilla gorilla	ENSGGOG00000024268	1 retrocopy	retro_ggor_189,
Loxodonta africana	ENSLAFG00000003044	1 retrocopy	retro_lafr_898,
Microcebus murinus	ENSMICG00000004639	1 retrocopy	retro_mmur_106,
Myotis lucifugus	ENSMLUG00000001319	1 retrocopy	retro_mluc_2075,
Macaca mulatta	ENSMMUG00000002888	1 retrocopy	retro_mmul_310,
Mustela putorius furo	ENSMPUG00000011896	1 retrocopy	retro_mputfur_46,
Mus musculus	ENSMUSG00000073139	1 retrocopy	retro_mmus_358,
Nomascus leucogenys	ENSNLEG00000013487	1 retrocopy	retro_nleu_2723,
Otolemur garnettii	ENSOGAG00000016414	1 retrocopy	retro_ogar_88,
Procavia capensis	ENSPCAG00000009160	1 retrocopy	retro_pcap_260,
Pongo abelii	ENSPPYG00000020809	1 retrocopy	retro_pabe_118,
Pteropus vampyrus	ENSPVAG00000013822	1 retrocopy	retro_pvam_30,
Rattus norvegicus	ENSRNOG00000011047	1 retrocopy	retro_rnor_6,
Sus scrofa	ENSSSCG00000012739	1 retrocopy	retro_sscr_494,
Ictidomys tridecemlineatus	ENSSTOG00000014484	1 retrocopy	retro_itri_8,
Tursiops truncatus	ENSTTRG00000000643	1 retrocopy	retro_ttru_868,