RetrogeneDB ID: retro_pabe_1438

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 17:19118672..19119256(+)
• Located in intron of: ENSPPYG00000008054

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_1438
GCCAAGGACACTCATGAGGACCATGATACTTCCACTGAGAATGCAGATGAGTCCAACCATGACCCTCAGTTTGAGCCAAT
AGTTTCTCTTCCTGAGCAAGAAATTAAAACGCTGGAGGAAGATGAAGAACTTTTAAAAATGCAGATGAAACTGTTCTGAT
TTGCCTCAGAGAAGGATCTCCCAGAATGGAAGGAGTGAGGCACCGGCAATGTCAAGCTCCTGAAACACAAGGAGAGGGGG
ACCATCCGCCTCCTCATGCGGAGGGACAAGACCCTGAAGATCTCTGCTAACCACTACTTCACGCTGATAACAGAGCTGAA
GCCCAACGTGGATAGTGACCATGCCTGGGTCTGGAACACCCACGCCGACTTCGCCAACGAGTGCCCCAAGCCAGAGCTGC
TGGCCATCCTCTTCCTGAATGTTGAGAATGCACAGAAATTCAAAACAAAGTTTGAAGAATGCAAGAAAGAGATCAGAGAG
AAAAGAAAGGATCGGGCAAAAATGATCATGCCAAAAAAGTGGCGGAAAAGCTTGAAGCTCTTTTGGTGGAGGAGGAGTCC
AAGGAGGATGCTGAGGAGAAGCAA

Alignment

ORF - retro_pabe_1438 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.42 %
• Parental protein coverage: 98.51 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AKDTHEDHDTSTENTDESNHDPQFEPIVSLPEQEIKTLEEDEEELFKMRAKLFRFASENDLPEWKERGTG
          AKDTHEDHDTSTEN.DESNHDPQFEPIVSLPEQEIKTLEEDEE.L.KM..KLF.FASE.DLPEWKE.GTG
Retrocopy AKDTHEDHDTSTENADESNHDPQFEPIVSLPEQEIKTLEEDEE-LLKMQMKLF*FASEKDLPEWKE*GTG

Parental  DVKLLKHKEKGAIRLLMRRDKTLKICANHYITPMMELKPNAGSDRAWVWNTHADFADECPKPELLAIRFL
          .VKLLKHKE.G.IRLLMRRDKTLKI.ANHY.T...ELKPN..SD.AWVWNTHADFA.ECPKPELLAI.FL
Retrocopy NVKLLKHKERGTIRLLMRRDKTLKISANHYFTLITELKPNVDSDHAWVWNTHADFANECPKPELLAILFL

Parental  NAENAQKFKTKFEECRKEIEEREK-KAGSGKNDHAEKVAEKLEALSVKEETKEDAEEKQ
          N.ENAQKFKTKFEEC.KEI..REK.K.GSGKNDHA.KVAEKLEAL.V.EE.KEDAEEKQ
Retrocopy NVENAQKFKTKFEECKKEI--REK<KKGSGKNDHAKKVAEKLEALLVEEESKEDAEEKQ

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	0.36 RPM	21.52 RPM
SRP007412_heart	0.09 RPM	5.21 RPM
SRP007412_kidney	0.20 RPM	10.97 RPM
SRP007412_liver	0.12 RPM	15.03 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1438 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1438 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1438 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,