RetrogeneDB ID: retro_mmul_1112

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 14:83305209..83306075(-)
• Located in intron of: ENSMMUG00000007921

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.2307
• Ensembl ID: ENSMMUG00000014809
• Aliases: HNRNPC, HNRPC
• Description: heterogeneous nuclear ribonucleoprotein C (C1/C2) [Source:RefSeq peptide;Acc:NP_001248162]

Sequence

>retro_mmul_1112
ATGGCCAGCAACGTTACCAACAAGACAGATCCTCGTTCCATGAACACCCGTGTATTCACTGGGAATCTCAACACTCTTGT
GGTCAAGAAATCTGATGTGGAGGCAATCTTTCCGAAGTATGGCAAAATTGTGGGCTGCTCTGTTCATAAGGGCTTTGCTT
CATTCAATATGTTAATGAGAGAAATGCCCAGGCTGCAGGAGAGGATGGCAGAATGATTGCTGGTCAGGTTTTAGATATTA
ACCTGACTGCAGCACCAAAACTGAACGGAGGAAAAGCAGGCGTGAAACAATCTGCAGCGATGTACCGCTCTTCTTTTGAC
CTGGACTATGATTTTCAGCGGGATTATTGTAATAGGAGGTACAGTTACCCAGCATGTGTACCTCCTCCTCCTCTTACTGC
TGGAGGTGTAGTGCCCTCGAAACATCCGTGTGTATCAGGAAACACCTCAAGAAGGGAAAAAAGTGGCTTCAATTTTAAGA
GTGGACAGCGGGTATCTTCCAAGTCTGGAAAGTTGAAAGGAGATGACCTTCAGGCTGTTAAGAAGGAATTGACCCAGATA
AAACAAAAAATGGATTATCTCCTGGAAAACCTGGAAAAAATTGAAAAGGAACTGAGCAAACAAGCAGTAGAGATGAAAAA
TAAGTCAGAAGAGGAGCAGAGCAGCAGCTCCTTGAAGAAAGACGAGACTAATTTGAAGTTGGAGTCTGAGGGGGGTGCAA
ATAACCCTGCTGAGGAGGGGGACCCACTGGATGATGATGATAATGAAGACTGGGGGGATGACCAGCTGGAATTGATCAAG
GATGAAGAAAAAGAGGCCGAGGAAGGAGAGGATGACAGAGACAGCGCCAATGGTGAGGATGACTCT

Alignment

ORF - retro_mmul_1112 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.27 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MASNVTNKTDPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHKGFA-FVQYVNERNARAAVAG
          MASNVTNKTDPRSMN.RVF.GNLNTLVVKKSDVEAIF.KYGKIVGCSVHKGFA.F.QYVNERNA.AA..G
Retrocopy MASNVTNKTDPRSMNTRVFTGNLNTLVVKKSDVEAIFPKYGKIVGCSVHKGFA<FIQYVNERNAQAA--G

Parental  EDGRMIAGQVLDINLAAEPKVNRGKAGVKRSAAEMYGSSFDLDYDFQRDYYDRMYSYPARVPPPPPIARA
          EDGRMIAGQVLDINL.A.PK.N.GKAGVK.SAA.MY.SSFDLDYDFQRDY..R.YSYPA.VPPPP..A..
Retrocopy EDGRMIAGQVLDINLTAAPKLNGGKAGVKQSAA-MYRSSFDLDYDFQRDYCNRRYSYPACVPPPPLTAGG

Parental  VVPSKRQRVSGNTSRRGKSGFNSKSGQRGSSKSGKLKGDDLQAIKKELTQIKQKVDSLLENLEKIEKEQS
          VVPSK...VSGNTSRR.KSGFN.KSGQR.SSKSGKLKGDDLQA.KKELTQ.................E.S
Retrocopy VVPSKHPCVSGNTSRREKSGFNFKSGQRVSSKSGKLKGDDLQAVKKELTQXXXXXXXXXXXXXXXXXELS

Parental  KQAVEMKNDKSEEEQSSSSVKKDETNVKMESEGGADDSAEEGDLLDDDDNEDRGDDQLELIKDDEKEAEE
          KQAVEMKN.KSEEEQSSSS.KKDETN.K.ESEGGA...AEEGD.LDDDDNED.GDDQLELIKD.EKEAEE
Retrocopy KQAVEMKN-KSEEEQSSSSLKKDETNLKLESEGGANNPAEEGDPLDDDDNEDWGDDQLELIKDEEKEAEE

Parental  GEDDRDSANGEDDS
          GEDDRDSANGEDDS
Retrocopy GEDDRDSANGEDDS

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	0.22 RPM	80.56 RPM
SRP007412_brain_prefrontal_cortex	0.08 RPM	97.97 RPM
SRP007412_cerebellum	0.19 RPM	61.93 RPM
SRP007412_heart	0.00 RPM	55.00 RPM
SRP007412_kidney	0.00 RPM	69.95 RPM
SRP007412_liver	0.00 RPM	47.46 RPM
SRP007412_testis	0.04 RPM	80.66 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1112 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1112 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1112 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_780

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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,