RetrogeneDB ID: retro_pabe_1263

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 15:76704326..76705202(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HNRNPC
• Ensembl ID: ENSPPYG00000005593
• Aliases: HNRNPC, HNRPC
• Description: Heterogeneous nuclear ribonucleoprotein C [Source:UniProtKB/Swiss-Prot;Acc:Q5RA82]

Sequence

>retro_pabe_1263
ATGGCCAGCAACGTTACCAACAAGACAGATCCTCGCTCCATGAACTCCCGTGTGTTCATTGGGAATCTCAACACTCTTGT
GGTCAAGAAATCTGATGTGGAGGCAATCTTTTCAAAGTATGGCAAAACTGTGGGCTGTGCTGTTCATAAGGGCTTTGCCT
TTATTCACTATTTTAATGAGAGAAATGCCCGGGCTGCTGGAGCAGGAGAGGATGGCAGAATGATTGCTGGCCAGGTTTTA
GATATTAACCTGGCTGCAGAGCCAAAAGTGAACTGAGGAAAAGCAGGCGTGAAACGATCTGCAGCAGGGATGTATAGCTC
CTCTTTTCACTTGGACTATGACTATCAAGGTGATTATGATGATACGATGTACAGTTACTCAGCACGCGTGCCTCCTCCTC
TTCCTATTGCTTGGGCTGTAGTGCTCTCAAAATGTCAGCGTGTATCAGGAAACAACTCACGAAGGGGCAAAAGTGGCCTC
AATTCTAAGAGTGGACAGCAGGGATCTTCCAAGTCTGGAAAGTTGAAAGGAGATGACCTTCAGGCCATTATGAAGGAGTT
GTCCCAGATAAAACAAAAAGTGGATTCTCTCCTGGAAAACCTGGAAAAAATTGAAAAGGAACAGAGCAAACAAGCAGTAC
AGATGAGGAATGGTAAGTCAGAAGAGGAGCAGAGCAGCAGCTCTGTGAAGAAAGATGAGACTAATGTGAAGATGGAGTCT
GAGGGGGTGCAGATGACTATGCTGAGAAGGGGGACCTACTGGATGATGATGATAATGAGGATGGGGGATGACCAGCTGGA
GTTGATCAAGGATGATGAAAAAGAGGCTGAGGAAGGAGAGGATGACAGAGACAGCACCAATGGCATGGATGACTCT

Alignment

ORF - retro_pabe_1263 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.07 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MASNVTNKTDPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHKGFAFVQYVNERNARAAVAGE
          MASNVTNKTDPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGK.VGC.VHKGFAF..Y.NERNARAA.AGE
Retrocopy MASNVTNKTDPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKTVGCAVHKGFAFIHYFNERNARAAGAGE

Parental  DGRMIAGQVLDINLAAEPKVNRGKAGVKRSAAEMYGSSFDLDYDFQRDYYDRMYSYPARVPPPPPIARAV
          DGRMIAGQVLDINLAAEPKVN.GKAGVKRSAA.MY.SSF.LDYD.Q.DY.D.MYSY.ARVPPP.PIA.AV
Retrocopy DGRMIAGQVLDINLAAEPKVN*GKAGVKRSAAGMYSSSFHLDYDYQGDYDDTMYSYSARVPPPLPIAWAV

Parental  VPSKRQRVSGNTSRRGKSGFNSKSGQRGSSKSGKLKGDDLQAIKKELTQIKQKVDSLLENLEKIEKEQSK
          V.SK.QRVSGN.SRRGKSG.NSKSGQ.GSSKSGKLKGDDLQAI.KEL.QIKQKVDSLLENLEKIEKEQSK
Retrocopy VLSKCQRVSGNNSRRGKSGLNSKSGQQGSSKSGKLKGDDLQAIMKELSQIKQKVDSLLENLEKIEKEQSK

Parental  QAVEMKNDKSEEEQSSSSVKKDETNVKMESE-GGADDSAEEGDLLDDDDNEDRG-DDQLELIKDDEKEAE
          QAV.M.N.KSEEEQSSSSVKKDETNVKMESE.GGADD.AE.GDLLDDDDNED.G.D.......D.....E
Retrocopy QAVQMRNGKSEEEQSSSSVKKDETNVKMESE<GGADDYAEKGDLLDDDDNEDGG>DQLELIKDDEKEAEE

Parental  EGEDDRDSANGEDDS
          .GEDDRDS.NG.DDS
Retrocopy -GEDDRDSTNGMDDS

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	0.17 RPM	198.11 RPM
SRP007412_cerebellum	3.04 RPM	239.43 RPM
SRP007412_heart	0.03 RPM	117.25 RPM
SRP007412_kidney	0.07 RPM	280.39 RPM
SRP007412_liver	0.03 RPM	272.08 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1263 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1263 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1263 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,