RetrogeneDB ID: retro_pabe_2161

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2b:120563934..120564705(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNF8
• Ensembl ID: ENSPPYG00000008911
• Aliases: None
• Description: SNF8, ESCRT-II complex subunit [Source:HGNC Symbol;Acc:17028]

Sequence

>retro_pabe_2161
TCCAAGGCCAAGTATAAGGAGCAAAGGACAGTCTTGGCTGAGGACCAGCTAGCCCAGATGTCAAACCAGTTGGGCATGTT
CAAGATCAACCTGGAGGAATTTGCCAGCAAGCCCAAGCAGGAGATCCGGAAGGATCCTGAGTTCCATGTGTAGTTCCAGG
ACATGTGTACAACCTTTAGGGTGGAGCCTTTGGCCTCTGGAAAAGGATTTTGATCTGAGATGCTGGGTGTGGGGGATTTT
TATTACGAACTAGGTGTCCACATTATCAAAGTGTGCCTGGTGCTGAGCATTGGAGTGGAGGTCCGATAACCCTGGAGGAA
CTACATCAACAGGTGTTAAAAGGAAGGGGCAAGTTCGCCCAGGATGTCAGTCAAGACGACCTGATCAGGGCCATCAAGAA
ACTAAAGGCACTTGGCACTGGCTTCAGCATCATCCCCATGAGTGGCACTTACCTCATTCAGTCTGTTCCAGCTGAATTCA
ATATGGATTACACCAAGGGGCTGCAGCTGGCAGAGAAAAATGGCTATTGACTGTCAGAGAGATCAAAGCCAGTCTTAAAT
GGGAGACCCAATGAGCGGGGCAAGTGCCAGAACCCCTGCTGAGAGAAGGGCTGGCGTGGCTGGACTTACAGGCCCCAGGG
GAGATCCACTACTGGCTGCCAGCTCTATTCACTGACCTCTACTCCCAGGAGATTACAGCTGAGGCAGCCAGAGAAGTCTT
CCCCTAAGTGTGGAAGGGCACACAGCAGCAGGCAGGGAGAAGCAGGGAGGC

Alignment

ORF - retro_pabe_2161 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.99 %
• Parental protein coverage: 93.19 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  AEAKYKERGTVLAEDQLAQMSKQLDMFKTNLEEFASKHKQEIRKNPEFRVQFQDMCATIGVDPLASGKGF
          ..AKYKE..TVLAEDQLAQMS.QL.MFK.NLEEFASK.KQEIRK.PEF.V.FQDMC.T..V.PLASGKGF
Retrocopy SKAKYKEQRTVLAEDQLAQMSNQLGMFKINLEEFASKPKQEIRKDPEFHV*FQDMCTTFRVEPLASGKGF

Parental  WSEMLGVGDFYYELGVQIIEVCLAL-KHRNGGLITLEELHQQVLKGRGKFAQDVSQDDLIRAIKKLKALG
          .SEMLGVGDFYYELGV.II.VCL.L..H..GG.ITLEELHQQVLKGRGKFAQDVSQDDLIRAIKKLKALG
Retrocopy *SEMLGVGDFYYELGVHIIKVCLVL<EHWSGGPITLEELHQQVLKGRGKFAQDVSQDDLIRAIKKLKALG

Parental  TGFGIIPVGGTYLIQSVPAELNMDHTVVLQLAEKNGY-VTVSEIKASLNWETERARQVLEHLLKEGLAWL
          TGF.IIP..GTYLIQSVPAE.NMD.T..LQLAEKNGY..TV.EIKASL.WET..A.QV.E.LL.EGLAWL
Retrocopy TGFSIIPMSGTYLIQSVPAEFNMDYTKGLQLAEKNGY<LTVREIKASLKWETQ*AGQVPEPLLREGLAWL

Parental  DLQAPGEAHYWLPALFTDLYSQEITAEEARE-SPPLTGVVEGHTAAGREGGGG
          DLQAPGE.HYWLPALFTDLYSQEITAE.ARE.S.PL...VEGHTAAGRE..GG
Retrocopy DLQAPGEIHYWLPALFTDLYSQEITAEAARE<SLPLS--VEGHTAAGREKQGG

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	0.11 RPM	25.21 RPM
SRP007412_cerebellum	0.12 RPM	22.25 RPM
SRP007412_heart	0.00 RPM	16.86 RPM
SRP007412_kidney	0.03 RPM	42.86 RPM
SRP007412_liver	0.00 RPM	23.93 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2161 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2161 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2161 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2394
Gorilla gorilla	retro_ggor_1816

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005062	1 retrocopy	retro_amel_164,
Canis familiaris	ENSCAFG00000016893	1 retrocopy	retro_cfam_1488,
Choloepus hoffmanni	ENSCHOG00000013760	1 retrocopy	retro_chof_1372,
Callithrix jacchus	ENSCJAG00000007322	2 retrocopies	retro_cjac_1175, retro_cjac_1922,
Echinops telfairi	ENSETEG00000000758	1 retrocopy	retro_etel_709,
Felis catus	ENSFCAG00000008944	2 retrocopies	retro_fcat_1291, retro_fcat_574,
Homo sapiens	ENSG00000159210	1 retrocopy	retro_hsap_2394,
Gorilla gorilla	ENSGGOG00000025290	1 retrocopy	retro_ggor_1816,
Macropus eugenii	ENSMEUG00000016638	1 retrocopy	retro_meug_663,
Mustela putorius furo	ENSMPUG00000015356	1 retrocopy	retro_mputfur_1425,
Mus musculus	ENSMUSG00000006058	1 retrocopy	retro_mmus_1050,
Nomascus leucogenys	ENSNLEG00000002743	1 retrocopy	retro_nleu_2520,
Oryctolagus cuniculus	ENSOCUG00000009156	2 retrocopies	retro_ocun_814, retro_ocun_996,
Pongo abelii	ENSPPYG00000008911	1 retrocopy	retro_pabe_2161 ,
Tarsius syrichta	ENSTSYG00000004576	1 retrocopy	retro_tsyr_843,