RetrogeneDB ID: retro_hsap_1624

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 16:11336538..11337406(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000263179
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: HNRNPC
• Ensembl ID: ENSG00000092199
• Aliases: HNRNPC, C1, C2, HNRNP, HNRPC, SNRPC
• Description: heterogeneous nuclear ribonucleoprotein C (C1/C2) [Source:HGNC Symbol;Acc:5035]

Sequence

>retro_hsap_1624
TCGCTCCATGAACGCGTGTTCGTTGGGAATCTCAACACTCTTGTGGTCAAGAAATCTGATGTGGAGGCAATCTTTTAGAA
GTATGGCAAAATTGTGGGCTGCGCTGTTCTTAAGGGCTTTGTTTTCATTCAGTATGTTAATGAGAGAAATGCCCGGGCCG
CTGTAGCAGCAGCAGATGGCAGAATAATCGCTGGCCAGGTTTTACATAGTAACCTGGCTGCAGAGCCAAAAGTGAACCGA
GGAAAAGCAGGTATGAAATGATCAGCAGTGGAGACGTACGGGTCAGAAACAGAACACCCTTCTCCATTCCTCTACTCAGC
TCCTCTTTTGACTTGGACTATGACTTTCAACGGGATTATGATAGGATGTACAGTTACCCAGCACGTGTACCTCCTCCTCC
TCCTATTGCTCGGGCTGTAGTGCCCTTGAAACATCAGCGTGTATCAGGAAACACCTCACAAAGGGGCAAAAGTGGCTTCA
ATTCTAAGAGTGGACAGCGGGGATCTTCCAAGTCTGGAAAGTTGAAAGGAGATGACCTTCAGGCCATTAAGCAGGAGTTG
ACCCAGATAAAACAAAAAGTGGATTCTCTCCTGGAAGACCCGGAAAAAATGGAAAAGAAACAGAGCAAACAAGCAGTAGA
GATGAAGAATGGTAAGTCAGAAGAGAAGCAGAGCAGCAGCTCACGTGAGACTCATGTGAAGATAGAGTCTGAAGGTGGTG
CAGATGACTCTGCTGAGGAGAGGGACCTACTGGATGATGAGGATAATGAAGATTGGGGGATGACCAGCTGGAGTTGATCA
AGGATGATGAAAAAGAGGCTGAGGAAGGAGAGGATGACAGAGACAGCACCAATGGTGAAGATGACTCT

Alignment

ORF - retro_hsap_1624 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.47 %
• Parental protein coverage: 96.08 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHKGFAFVQYVNERNARAAVAGEDGRMIAGQVLDI
          S...RVF.GNLNTLVVKKSDVEAIF.KYGKIVGC.V.KGF.F.QYVNERNARAAVA..DGR.IAGQVL..
Retrocopy SLHERVFVGNLNTLVVKKSDVEAIF*KYGKIVGCAVLKGFVFIQYVNERNARAAVAAADGRIIAGQVLHS

Parental  NLAAEPKVNRGKAGVKRSAAEMYGSVTEHPSP-SPLLSSSFDLDYDFQRDYYDRMYSYPARVPPPPPIAR
          NLAAEPKVNRGKAG.K.SA.E.YGS.TEHPSP..PLLSSSFDLDYDFQRD.YDRMYSYPARVPPPPPIAR
Retrocopy NLAAEPKVNRGKAGMK*SAVETYGSETEHPSP<IPLLSSSFDLDYDFQRD-YDRMYSYPARVPPPPPIAR

Parental  AVVPSKRQRVSGNTSRRGKSGFNSKSGQRGSSKSGKLKGDDLQAIKKELTQIKQKVDSLLENLEKIEKEQ
          AVVP.K.QRVSGNTS.RGKSGFNSKSGQRGSSKSGKLKGDDLQAIK.ELTQIKQKVDSLLE..EK.EK.Q
Retrocopy AVVPLKHQRVSGNTSQRGKSGFNSKSGQRGSSKSGKLKGDDLQAIKQELTQIKQKVDSLLEDPEKMEKKQ

Parental  SKQAVEMKNDKSEEEQSSSSVKKDETNVKMESEGGADDSAEEGDLLDDDDNED-RGDDQLELIKDDEKEA
          SKQAVEMKN.KSEE.QSSSS....ET.VK.ESEGGADDSAEE.DLLDD.DNED..GDDQLELIKDDEKEA
Retrocopy SKQAVEMKNGKSEEKQSSSS---RETHVKIESEGGADDSAEERDLLDDEDNED<LGDDQLELIKDDEKEA

Parental  EEGEDDRDSANGEDDS
          EEGEDDRDS.NGEDDS
Retrocopy EEGEDDRDSTNGEDDS

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	252.87 RPM
bodymap2_adrenal	0.27 RPM	354.06 RPM
bodymap2_brain	0.00 RPM	268.86 RPM
bodymap2_breast	0.06 RPM	217.61 RPM
bodymap2_colon	0.00 RPM	440.95 RPM
bodymap2_heart	0.00 RPM	106.54 RPM
bodymap2_kidney	0.06 RPM	268.64 RPM
bodymap2_liver	0.13 RPM	125.01 RPM
bodymap2_lung	0.02 RPM	411.16 RPM
bodymap2_lymph_node	0.00 RPM	414.78 RPM
bodymap2_ovary	0.15 RPM	474.73 RPM
bodymap2_prostate	0.12 RPM	360.76 RPM
bodymap2_skeletal_muscle	0.00 RPM	156.20 RPM
bodymap2_testis	0.41 RPM	351.48 RPM
bodymap2_thyroid	0.11 RPM	334.99 RPM
bodymap2_white_blood_cells	0.08 RPM	467.98 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_1624 was not detected

EST

No EST(s) were mapped for retro_hsap_1624 retrocopy.

TSS

No TSS is located nearby retro_hsap_1624 retrocopy 5' end.

Lab

retro_hsap_1624 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_1624 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 45 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000011396	2 retrocopies	retro_btau_1084, retro_btau_1142,
Canis familiaris	ENSCAFG00000005504	1 retrocopy	retro_cfam_1140,
Homo sapiens	ENSG00000092199	2 retrocopies	retro_hsap_1624 , retro_hsap_3740,
Homo sapiens	ENSG00000125970	1 retrocopy	retro_hsap_37,
Gorilla gorilla	ENSGGOG00000023015	1 retrocopy	retro_ggor_1046,
Microcebus murinus	ENSMICG00000007682	2 retrocopies	retro_mmur_1439, retro_mmur_863,
Macaca mulatta	ENSMMUG00000014809	4 retrocopies	retro_mmul_1112, retro_mmul_205, retro_mmul_468, retro_mmul_503,
Mustela putorius furo	ENSMPUG00000000164	2 retrocopies	retro_mputfur_231, retro_mputfur_241,
Mus musculus	ENSMUSG00000060373	1 retrocopy	retro_mmus_1388,
Nomascus leucogenys	ENSNLEG00000014362	2 retrocopies	retro_nleu_1828, retro_nleu_59,
Oryctolagus cuniculus	ENSOCUG00000015029	1 retrocopy	retro_ocun_138,
Otolemur garnettii	ENSOGAG00000012543	1 retrocopy	retro_ogar_165,
Pongo abelii	ENSPPYG00000005593	6 retrocopies	retro_pabe_1116, retro_pabe_1263, retro_pabe_1342, retro_pabe_2, retro_pabe_722, retro_pabe_780,
Pan troglodytes	ENSPTRG00000006118	2 retrocopies	retro_ptro_1089, retro_ptro_2539,
Rattus norvegicus	ENSRNOG00000011621	1 retrocopy	retro_rnor_922,
Tupaia belangeri	ENSTBEG00000011514	11 retrocopies	retro_tbel_1738, retro_tbel_2114, retro_tbel_2475, retro_tbel_2838, retro_tbel_2849, retro_tbel_3094, retro_tbel_3293, retro_tbel_3776, retro_tbel_3903, retro_tbel_3937, retro_tbel_818,
Tarsius syrichta	ENSTSYG00000003305	3 retrocopies	retro_tsyr_1004, retro_tsyr_1326, retro_tsyr_1411,
Tursiops truncatus	ENSTTRG00000016055	2 retrocopies	retro_ttru_1299, retro_ttru_1490,