RetrogeneDB ID: retro_pabe_1111

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 14:55847659..55848199(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CHMP4B
• Ensembl ID: ENSPPYG00000010931
• Aliases: None
• Description: charged multivesicular body protein 4B [Source:HGNC Symbol;Acc:16171]

Sequence

>retro_pabe_1111
GAGATGTTAACCGAGAAACAGGAGTTCCTGGAGAAGAAAATCGAGCAGAGGCACGGCACTAAAAACAAGTGCGCGGCCCA
CCAGACACTGAAGCATAAAAAGAGGTATGAGAAGCAGTTGGCGCACATCGACGGCACATTATCAACCATCGAGCAGCAGG
CCCTGAAGAATGCCAACACCAATACCGAGGTGCTCAAGAACATGGGCTCTGCCGCCCAGGCCAAGAAGGCGGCCCATGAC
AACATGGACATCGATAAAGTTGATGAGTTAATGCAGGACATTGCTGACCAGCAAGAACTTGGGGAGGAGATTTCAACAGC
AATTTCAAAACCCGTAGGGTTTGGAGAAAAGTCTGACGAGGATGAGCTCATGGCGGAGTTAGAAGAACTAGAACAGGAGG
AACTAGACAAGAATTTGCTGGAAATCAGTGGCCCCGAAACAGTCTCTCTACCAAATGTTCCCTCTTATAGCCCTACCATC
AAAACCTGCCAAGAAGAGGAAGACGACGACATGAAGGATTTGGAGAACTGGGCTGGGTCC

Alignment

ORF - retro_pabe_1111 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.42 %
• Parental protein coverage: 87.14 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QRLRDTEEMLSKKQEFLE-KKIEQEALQALKRKKRYEKQLAQIDGTLSTIEFQREALENANTNTEVLKNM
          ..L....E.L.KK.E.....K....A.Q.LK.KKRYEKQLA.IDGTLSTIE....AL.NANTNTEVLKNM
Retrocopy EMLTEKQEFLEKKIEQRHGTKNKCAAHQTLKHKKRYEKQLAHIDGTLSTIE--QQALKNANTNTEVLKNM

Parental  GYAAKAMKAAHDNMDIDKVDELMQDIADQQELAEEISTAISKPVGFGEEFDEDELMAELEELEQEELDKN
          G.AA.A.KAAHDNMDIDKVDELMQDIADQQEL.EEISTAISKPVGFGE..DEDELMAELEELEQEELDKN
Retrocopy GSAAQAKKAAHDNMDIDKVDELMQDIADQQELGEEISTAISKPVGFGEKSDEDELMAELEELEQEELDKN

Parental  LLEISGPETVPLPNVPS-IALPSKPAKKK-EEEDDDMKELENWAGS
          LLEISGPETV.LPNVPS.IALPSKPAKK..E..D..MK.LENWAGS
Retrocopy LLEISGPETVSLPNVPS>IALPSKPAKKR<EDDD--MKDLENWAGS

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	0.00 RPM	128.11 RPM
SRP007412_cerebellum	0.36 RPM	58.49 RPM
SRP007412_heart	0.24 RPM	39.59 RPM
SRP007412_kidney	0.73 RPM	72.39 RPM
SRP007412_liver	0.52 RPM	56.86 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1111 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1111 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1111 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1339
Pan troglodytes	retro_ptro_915

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009038	1 retrocopy	retro_amel_1612,
Canis familiaris	ENSCAFG00000007478	1 retrocopy	retro_cfam_1304,
Choloepus hoffmanni	ENSCHOG00000007288	1 retrocopy	retro_chof_2518,
Equus caballus	ENSECAG00000008311	1 retrocopy	retro_ecab_496,
Felis catus	ENSFCAG00000025893	1 retrocopy	retro_fcat_1835,
Homo sapiens	ENSG00000101421	1 retrocopy	retro_hsap_1339,
Gorilla gorilla	ENSGGOG00000007775	1 retrocopy	retro_ggor_29,
Macaca mulatta	ENSMMUG00000008084	1 retrocopy	retro_mmul_2178,
Mustela putorius furo	ENSMPUG00000017821	2 retrocopies	retro_mputfur_1302, retro_mputfur_697,
Nomascus leucogenys	ENSNLEG00000010020	1 retrocopy	retro_nleu_1822,
Pongo abelii	ENSPPYG00000005691	1 retrocopy	retro_pabe_1937,
Pongo abelii	ENSPPYG00000010931	1 retrocopy	retro_pabe_1111 ,
Pan troglodytes	ENSPTRG00000013408	1 retrocopy	retro_ptro_915,
Pteropus vampyrus	ENSPVAG00000010293	1 retrocopy	retro_pvam_973,
Rattus norvegicus	ENSRNOG00000046585	1 retrocopy	retro_rnor_61,
Tarsius syrichta	ENSTSYG00000013212	1 retrocopy	retro_tsyr_1453,