RetrogeneDB ID: retro_pabe_943

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 12:77471927..77472497(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RANBP1
• Ensembl ID: ENSPPYG00000011593
• Aliases: None
• Description: RAN binding protein 1 [Source:HGNC Symbol;Acc:9847]

Sequence

>retro_pabe_943
GCTGCCGCCAAGGACACTCATGAAGACCATGATACTTCCACTGAGAATACAGACGAGTACAACCATGACCCTCAGTTTGA
GCCAGTAGTTTCTCTTCCTGAGCAAGAAATTAAAACGCTGAAAGATGATGAAGAGGAACTTTTTAAAATGTGGGCAAAAC
TGTTCTGATTTGCCTCAGAGAACGCTCTCCCAGAATGGAAGGAGGGAGGCACTGGTGACGTCAAGCTCCTGAAGCACAAG
GAGAAAGGGGCCATCCACCTCCTCATGCAGAGGGACAAGACCCTGAATATCTGTGCCAACCACCACATCAGGCCGATGAT
GGAGCTGAAGCCCAGCGCAGGTAGCGAGGGTGCCTGGGTCTGGAACACCTATGCTGACTTCACCGAGGAGTACCCCAAGC
CAGAGCTGCTGGCCATCTGCTTCCTGAATGCTGAGAATGCACAGAAATTCAAAACAAAGTTTGAAGAATGCAGGAAAGAG
ATCGAAGAGAGAGAAAAGAAAGCAAGATCAGGCAAAAACGATCATGCCAAAAAAGTGGCGGAGAATCTCGCTAGAAGCTC
TCTTGGTGAA

Alignment

ORF - retro_pabe_943 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.74 %
• Parental protein coverage: 94.53 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AAAKDTHEDHDTSTENTDESNHDPQFEPIVSLPEQEIKTLEEDEEELFKMRAKLFRFASENDLPEWKERG
          AAAKDTHEDHDTSTENTDE.NHDPQFEP.VSLPEQEIKTL..DEEELFKM.AKLF.FASEN.LPEWKE.G
Retrocopy AAAKDTHEDHDTSTENTDEYNHDPQFEPVVSLPEQEIKTLKDDEEELFKMWAKLF*FASENALPEWKEGG

Parental  TGDVKLLKHKEKGAIRLLMRRDKTLKICANHYITPMMELKPNAGSDRAWVWNTHADFADECPKPELLAIR
          TGDVKLLKHKEKGAI.LLM.RDKTL.ICANH.I.PMMELKP.AGS..AWVWNT.ADF..E.PKPELLAI.
Retrocopy TGDVKLLKHKEKGAIHLLMQRDKTLNICANHHIRPMMELKPSAGSEGAWVWNTYADFTEEYPKPELLAIC

Parental  FLNAENAQKFKTKFEECRKEIEEREKKAGSGKNDHAEKVAEKLEALSVKE
          FLNAENAQKFKTKFEECRKEIEEREKKA.SGKNDHA.KVAE.L...S..E
Retrocopy FLNAENAQKFKTKFEECRKEIEEREKKARSGKNDHAKKVAENLARSSLGE

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	0.06 RPM	17.31 RPM
SRP007412_cerebellum	0.00 RPM	21.52 RPM
SRP007412_heart	0.00 RPM	5.21 RPM
SRP007412_kidney	0.00 RPM	10.97 RPM
SRP007412_liver	0.00 RPM	15.03 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_943 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_943 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_943 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 40 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000010749	1 retrocopy	retro_cjac_2619,
Cavia porcellus	ENSCPOG00000002962	1 retrocopy	retro_cpor_1249,
Dipodomys ordii	ENSDORG00000011317	2 retrocopies	retro_dord_241, retro_dord_602,
Echinops telfairi	ENSETEG00000015996	2 retrocopies	retro_etel_1018, retro_etel_1518,
Homo sapiens	ENSG00000099901	2 retrocopies	retro_hsap_1727, retro_hsap_4797,
Gorilla gorilla	ENSGGOG00000000784	1 retrocopy	retro_ggor_170,
Macropus eugenii	ENSMEUG00000016620	8 retrocopies	retro_meug_1064, retro_meug_1553, retro_meug_1670, retro_meug_1795, retro_meug_272, retro_meug_422, retro_meug_657, retro_meug_753,
Myotis lucifugus	ENSMLUG00000017535	1 retrocopy	retro_mluc_1429,
Macaca mulatta	ENSMMUG00000020100	1 retrocopy	retro_mmul_1215,
Monodelphis domestica	ENSMODG00000010312	5 retrocopies	retro_mdom_1290, retro_mdom_1397, retro_mdom_1406, retro_mdom_1996, retro_mdom_288,
Mus musculus	ENSMUSG00000005732	1 retrocopy	retro_mmus_3632,
Nomascus leucogenys	ENSNLEG00000005684	2 retrocopies	retro_nleu_2991, retro_nleu_934,
Otolemur garnettii	ENSOGAG00000034333	2 retrocopies	retro_ogar_1428, retro_ogar_2735,
Pongo abelii	ENSPPYG00000011593	4 retrocopies	retro_pabe_1438, retro_pabe_1470, retro_pabe_3731, retro_pabe_943 ,
Rattus norvegicus	ENSRNOG00000001884	4 retrocopies	retro_rnor_1817, retro_rnor_811, retro_rnor_884, retro_rnor_907,
Sarcophilus harrisii	ENSSHAG00000006873	1 retrocopy	retro_shar_9,
Ictidomys tridecemlineatus	ENSSTOG00000026840	2 retrocopies	retro_itri_1579, retro_itri_345,