RetrogeneDB ID: retro_ptro_2539

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 7:62745915..62746832(+)
• 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_2539
ATGGCCAGCAATGTTACCAACAGAACAGATCCTCGCTCCATGAACTCCCATGTGTTCACTGGAAATCTGAACACTCTTGT
GGTCAAGAAGTGTGATGTGGAGGCAATCTTTTCGATGTGCAGCAAAATTGTGGGTTGCTCGGTTCATAAGGGCTTTGCCT
TTGTTCAACAGGTGAATGAGAGAAATGCCCCGGCTGCTGTAGAAGAGAGAAGGGCAGAATAATTGCTGGCCAGGTTTTAG
ATATTAACCTGGCTGCAGAGCCAAAAGTGAACGGAGGAAAAGCAGGTGTGAAATGATCTGCAGCGATGTATGGGTCAGTA
ACAGAACACCCTTCTCCATCGCCTCTATTCAGCTCCTCTCTTGACTTGGACTATGACTTTCAACGGGATTATTGTGAAAG
GATGTACAGTTGCCCAGCACATTTTCCTCCTCCTCCTCCTCATCCTCCTCCTCCTATTGCTTAGGCTGTAGTGCCCTCGA
AACGTCAGCATGTTTCAGAAAACACCTCATGAAGGGGCAAAAGTGGCTTCAATTCTAAGAGTGGACAGCAGGGATCTTCC
AAGTCTGGAAAGTTGAAAGGAGATGATGACCTTTAGGCCATTAAGAAGGAACTGACCCAGATAAAACAAAAGGTGGATTC
AACCCTGGAAAACCTGGAAAAATTTAAAAGGAACAGAGCAAACAAGCAGTAGAGATGAAGAATGGTAAGTGAGAAGAGGA
ACAGAGCAGGAGCTCAGTGAAGAAAAATGAGATTAATGTGAAGTCTGAGGGGGGCGCAGATGACTCTGCTGAGGAGGGGT
ATCTACTGGATGATGATGATAATGAAGGTGGGGGATGGCCAGCTGGAGTTGACCAAGGATGAAAAAGAGGCTGAGGAAGG
AGAGGATGACAGAGACAGCGCCAATGGCAAAAATGAC

Alignment

ORF - retro_ptro_2539 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.16 %
• Parental protein coverage: 99.67 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MASNVTNKTDPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHKGFAFVQYVNERNARAAVAG-
          MASNVTN.TDPRSMNS.VF.GNLNTLVVKK.DVEAIFS...KIVGCSVHKGFAFVQ.VNERNA.AAV...
Retrocopy MASNVTNRTDPRSMNSHVFTGNLNTLVVKKCDVEAIFSMCSKIVGCSVHKGFAFVQQVNERNAPAAVEE<

Parental  EDGRMIAGQVLDINLAAEPKVNRGKAGVKRSAAEMYGSVTEHPSPSPL----LSSSFDLDYDF-QRDYYD
          E.GR.IAGQVLDINLAAEPKVN.GKAGVK.SAA.MYGSVTEHPSPSPL....L....D...D...R.Y..
Retrocopy EKGRIIAGQVLDINLAAEPKVNGGKAGVK*SAA-MYGSVTEHPSPSPLFSSSLDLDYDFQRDYCERMYSC

Parental  RMYSYPARVPPPPPIARAVVPSKRQRVSGNTSRRGKSGFNSKSGQRGSSKSGKLKGDD-LQAIKKELTQI
          ..............IA.AVVPSKRQ.VS.NTS.RGKSGFNSKSGQ.GSSKSGKLKGDD.L.AIKKELTQI
Retrocopy PAHXXXXXXXXXXXIA*AVVPSKRQHVSENTS*RGKSGFNSKSGQQGSSKSGKLKGDDDL*AIKKELTQI

Parental  KQKVDSLLENLEKIE-KEQSKQAVEMKNDKSEEEQSSSSVKKDETNVKMESEGGADDSAEEGDLLDDDDN
          KQKVDS.LENLEK...KEQSKQAVEMKN.K.EEEQS.SSVKK.E.NVK..SEGGADDSAEEG.LLD.DD.
Retrocopy KQKVDSTLENLEKFK<KEQSKQAVEMKNGK*EEEQSRSSVKKNEINVK--SEGGADDSAEEGYLLD-DDD

Parental  EDRG-DDQLELIKDDEKEAEEGEDDRDSANGEDD
          ...G.D.QLEL.K.DEKEAEEGEDDRDSANG..D
Retrocopy NEGG>DGQLELTK-DEKEAEEGEDDRDSANGKND

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	1.16 RPM	151.63 RPM
SRP007412_cerebellum	2.62 RPM	216.88 RPM
SRP007412_heart	1.63 RPM	122.36 RPM
SRP007412_kidney	0.76 RPM	204.14 RPM
SRP007412_liver	0.69 RPM	211.07 RPM
SRP007412_testis	0.95 RPM	297.71 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2539 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2539 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2539 has 0 orthologous retrocopies within eutheria group .

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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,