RetrogeneDB ID: retro_ptro_1089

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 16:11413354..11414222(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: HNRNPC
• Ensembl ID: ENSPTRG00000006118
• Aliases: HNRNPC, HNRPC
• Description: heterogeneous nuclear ribonucleoprotein C (C1/C2) [Source:RefSeq peptide;Acc:NP_001233371]

Sequence

>retro_ptro_1089
TCGCTCCATGAACGCGTGTTCGTTGGGAATCTCAACACTCTTGTGGTCAAGAAATCTGATGTGGAGGCAATCTTTTAGAA
GTATGGCAAAATTGTGGGCTGCGCTGTTCTTAAGGGCTTTGTTTTCATTCAGTATGTTAATGAGAGAAATGCCTGGGCCG
CTGTAGCAGCAGCAGATGGCAGAATAATCGCTGGCCAGGTTTTAGATAGTAACCTGGCTGCAGAGCCAAAAGTGAACCGA
GGAAAAGCAGGTATGAAATGATCAGCAGTGGAGACGTACGGGTCAGAAACAGAACACCCTTCTCCATTCCTCTACTCAGC
TCCTCTTTTGACTTGGACTATGACTTTCAACGGGATTATGATAGGATGTACAGTTACCCAGCACGTGTACCTCCTCCTCC
TCCTATTGCTCGGGCTGTAGTGGCCTTGAAACATCAGCGTGTATCAGGAAACACCTCACAAAGGGGCAAAAGTGGCTTCA
ATTCTAAGAGTGGACAGCGGGGATCTTCCAAGTCTGGAAAGTTGAAAGGAGATGACCTTCAGGCCATTAAGCAGGAGTTG
ACCCAGATAAAACAAAAAGTGGATTCTCTCCTGGAAGACCCGGAAAAAATGGAAAAGAAACAGAGCAAACAAGCAGTAGA
GATGAAGAATGGTAAGTCAGAAGAGAAGCAGAGCAGCAGCTCACGTGAGACTCATGTGAAGATAGAGTCTGAAGGTGGTG
CAGATGACTCTGCTGAGGAGAGGGACCCACTGGATGCTGAGGATAATGAAGATTGGGGGATGACCAGCTGGAGTTGATCA
AGGATGATGAAAAAGAGGCTGAGGAAGGAGAGGATGACAGAGACAGCACCAATGGTGAAGATGACTCT

Alignment

ORF - retro_ptro_1089 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.46 %
• 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.QYVNERNA.AAVA..DGR.IAGQVLD.
Retrocopy SLHERVFVGNLNTLVVKKSDVEAIF*KYGKIVGCAVLKGFVFIQYVNERNAWAAVAAADGRIIAGQVLDS

Parental  NLAAEPKVNRGKAGVKRSAAEMYGSVTEHPSPS-PLLSSSFDLDYDFQRDYYDRMYSYPARVPPPPPIAR
          NLAAEPKVNRGKAG.K.SA.E.YGS.TEHPSP..PLLSSSFDLDYDFQRDY.DRMYSYPARVPPPPPIAR
Retrocopy NLAAEPKVNRGKAGMK*SAVETYGSETEHPSPF<PLLSSSFDLDYDFQRDY-DRMYSYPARVPPPPPIAR

Parental  AVVPSKRQRVSGNTSRRGKSGFNSKSGQRGSSKSGKLKGDDLQAIKKELTQIKQKVDSLLENLEKIEKEQ
          AVV..K.QRVSGNTS.RGKSGFNSKSGQRGSSKSGKLKGDDLQAIK.ELTQIKQKVDSLLE..EK.EK.Q
Retrocopy AVVALKHQRVSGNTSQRGKSGFNSKSGQRGSSKSGKLKGDDLQAIKQELTQIKQKVDSLLEDPEKMEKKQ

Parental  SKQAVEMKNDKSEEEQSSSSVKKDETNVKMESEGGADDSAEEGDLLDDDDNED-RGDDQLELIKDDEKEA
          SKQAVEMKN.KSEE.QSSSS....ET.VK.ESEGGADDSAEE.D.LD..DNED..GDDQLELIKDDEKEA
Retrocopy SKQAVEMKNGKSEEKQSSSS---RETHVKIESEGGADDSAEERDPLDAEDNED<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
SRP007412_brain_prefrontal_cortex	0.04 RPM	151.63 RPM
SRP007412_cerebellum	0.11 RPM	216.88 RPM
SRP007412_heart	0.03 RPM	122.36 RPM
SRP007412_kidney	0.05 RPM	204.14 RPM
SRP007412_liver	0.03 RPM	211.07 RPM
SRP007412_testis	0.63 RPM	297.71 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1089 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1089 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1089 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_1342

---

Parental genes homology:

Parental genes homology involve 17 parental genes, and 44 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,
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,