RetrogeneDB ID: retro_pabe_2498

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 4:191664158..191664826(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: VTI1B
• Ensembl ID: ENSPPYG00000005927
• Aliases: None
• Description: vesicle transport through interaction with t-SNAREs 1B [Source:HGNC Symbol;Acc:17793]

Sequence

>retro_pabe_2498
ATGGCCACCTCCGCTGCCTCCTTGGAGCGTTTCAAGAAGCTGCACGAAATCTTCTGATGCCTCCATGAAGACCTACAAGG
GGTGCCTGAGCGGCTGCTGGGGACGGCAGGGACCGAAGATAAGTTGATCAGGGATTTTGATGAAAAGCAACAGGAAGCAA
ATGAAATGCTGGCGGGGATGGAGGAGGAGCTACGTTATGCACCCCTGTCTTTCCGTAAGCCCATGATGTCTGAGCTTCGA
AACTACCAGAAGGCCTTGCCAAACTCCATCAGGAGGTGAGAAGCACGCCTCTGACAGCCACACCAGGAGGGCGAGGAGAC
ATGAAATATGGCATATATGCTGTAGAGGATGAGCATATGAATTGGCTACAGTCTCAAAGGGCAATGCTTCTGCAAGGCCC
TGAAAGCCTGAACTGGGCCACCCAAAATATTGAACGTTCTCATCAGATTGCCACGGAGACTGACCAGATTCGCTCAGAAA
CCACAGAAGAGCTGGGGGAACAACGAGACCATTTAGAACGCACCAAGAGTAGACTGGTAAACACAACTGAAAACTTGAAC
AAAAGTCAAAAGATTCTCCGTTCAATGTCCAGAAAAGTGACAACCAACGAGCTGCTGCTTTCCATCATCATCTTACTGGA
GCTCGCCATCCTGGGAGGCCTGGTTTAC

Alignment

ORF - retro_pabe_2498 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.28 %
• Parental protein coverage: 96.98 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAASAASSEHFEKLHEIFRGLHEDLQGVPERLLGTAGTEEKKKLIRDFDEKQQEANETLAEMEEELRYAP
          MA.SAAS.E.F.KLHEIF..LHEDLQGVPERLLGTAGTE.K..LIRDFDEKQQEANE.LA.MEEELRYAP
Retrocopy MATSAASLERFKKLHEIF*CLHEDLQGVPERLLGTAGTEDK--LIRDFDEKQQEANEMLAGMEEELRYAP

Parental  LSFRNPMMSKLRNYRK-DLAKLHREVRSTPLTATPGGRGDMKYGIYAVENEHMNRLQSQRAMLLQGTESL
          LSFR.PMMS.LRNY.K..LAKLH.EVRSTPLTATPGGRGDMKYGIYAVE.EHMN.LQSQRAMLLQG.ESL
Retrocopy LSFRKPMMSELRNYQK<GLAKLHQEVRSTPLTATPGGRGDMKYGIYAVEDEHMNWLQSQRAMLLQGPESL

Parental  NRATQSIERSHRIATETDQIGSEIIEELGEQRDQLERTKSRLVNTSENLSKSRKILRSMSRKVTTNKLLL
          N.ATQ.IERSH.IATETDQI.SE..EELGEQRD.LERTKSRLVNT.ENL.KS.KILRSMSRKVTTN.LLL
Retrocopy NWATQNIERSHQIATETDQIRSETTEELGEQRDHLERTKSRLVNTTENLNKSQKILRSMSRKVTTNELLL

Parental  SIIILLELAILGGLVY
          SIIILLELAILGGLVY
Retrocopy SIIILLELAILGGLVY

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	0.28 RPM	80.61 RPM
SRP007412_cerebellum	0.73 RPM	47.42 RPM
SRP007412_heart	0.24 RPM	29.11 RPM
SRP007412_kidney	0.07 RPM	83.36 RPM
SRP007412_liver	0.03 RPM	40.30 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2498 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2498 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2498 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 38 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015263	1 retrocopy	retro_cjac_1439,
Dasypus novemcinctus	ENSDNOG00000003643	2 retrocopies	retro_dnov_1503, retro_dnov_2031,
Dipodomys ordii	ENSDORG00000015939	2 retrocopies	retro_dord_52, retro_dord_716,
Echinops telfairi	ENSETEG00000006101	1 retrocopy	retro_etel_783,
Felis catus	ENSFCAG00000014090	1 retrocopy	retro_fcat_1855,
Homo sapiens	ENSG00000100568	3 retrocopies	retro_hsap_1002, retro_hsap_2682, retro_hsap_3013,
Gorilla gorilla	ENSGGOG00000005620	2 retrocopies	retro_ggor_1871, retro_ggor_797,
Macropus eugenii	ENSMEUG00000004910	2 retrocopies	retro_meug_499, retro_meug_697,
Microcebus murinus	ENSMICG00000010843	1 retrocopy	retro_mmur_849,
Myotis lucifugus	ENSMLUG00000011184	3 retrocopies	retro_mluc_1299, retro_mluc_2393, retro_mluc_781,
Macaca mulatta	ENSMMUG00000015866	1 retrocopy	retro_mmul_1420,
Mustela putorius furo	ENSMPUG00000007130	1 retrocopy	retro_mputfur_1516,
Nomascus leucogenys	ENSNLEG00000000780	4 retrocopies	retro_nleu_1184, retro_nleu_2241, retro_nleu_231, retro_nleu_83,
Pongo abelii	ENSPPYG00000005927	5 retrocopies	retro_pabe_2298, retro_pabe_2498 , retro_pabe_2602, retro_pabe_845, retro_pabe_974,
Pan troglodytes	ENSPTRG00000006468	3 retrocopies	retro_ptro_1808, retro_ptro_2037, retro_ptro_751,
Pteropus vampyrus	ENSPVAG00000011671	3 retrocopies	retro_pvam_132, retro_pvam_592, retro_pvam_797,
Tupaia belangeri	ENSTBEG00000003049	1 retrocopy	retro_tbel_3432,
Tarsius syrichta	ENSTSYG00000007688	2 retrocopies	retro_tsyr_1662, retro_tsyr_94,