RetrogeneDB ID: retro_pabe_1427

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 17:4202730..4203343(+)
• Located in intron of: ENSPPYG00000007831

Retrocopy information

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

Parental gene information

• Parental gene symbol: MFSD1
• Ensembl ID: ENSPPYG00000014247
• Aliases: None
• Description: major facilitator superfamily domain-containing protein 1 [Source:RefSeq peptide;Acc:NP_001127485]

Sequence

>retro_pabe_1427
CTTTTGATGCTGTTATTGATGTGCCTCCTTGGCTTCAGCAGCTATTTTTGCTATAATAATCCTGCTCCCCTTCAGACTCA
GGATAAACAGAATAGGCAGGTGAACACCATGAAATTCATGCTGCTATATGCCTGGTATTCTTGGCCCAATGTAGTTTTGT
GTTTCTTTGGTGGCTTTTTAAAAGACCGAGTATTTGGAATATGATGGGGCACAATTACTTTTAGCTGTTTTATTTGCATT
GGACAGGTTGTTTTGTTCTGGGTGGAATATTTAATGTTTTTTGGCTGATGAAATTTGAAAGATTTGTGTTTGGATTGGTG
GGGAGTGCTCAGCAGTTGCCCAGGATACATATGCTGTGAGCTGGTTTAAAGACCAAGAATTAAACCTGGTGTCTGGACTC
CAACAATTTAGCATGGCTAGAATTGGAAGTATAGTAGACATGAACTTCATGAGTTGGCTGTACTCTAAGATTGAAGCTTC
GTGGGGTTCTGCCGGTCCCACAACCCCTGGGGTCACACTTCAGATTGGGGGTATAAAATGTATTCTTTCACTCATCTGTG
CCCTCCTTGGCTCTCGCTTACTTAGATCTGAGAGAATCCTTCATAAAGAACAA

Alignment

ORF - retro_pabe_1427 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.37 %
• Parental protein coverage: 56.94 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LLVLLLMCFLGFGSYFCYDNPAALQTQVKRDMQVNTTKFMLLYAWYSWPNVVLCFFGGFLIDRVFGIRWG
          LL.LLLMC.LGF.SYFCY.NPA.LQTQ.K...QVNT.KFMLLYAWYSWPNVVLCFFGGFL.DRVFGI.WG
Retrocopy LLMLLLMCLLGFSSYFCYNNPAPLQTQDKQNRQVNTMKFMLLYAWYSWPNVVLCFFGGFLKDRVFGI*WG

Parental  TIIFSCFVCIGQVV-FALGGIFNVFWLMEFGRFVFG-IGGESLAVAQNTYAVSWFKGKELNLVFGL-QLS
          TI.FSCF.CIGQVV.F.LGGIFNVFWLM.F.RFVFG.IGGE..AVAQ.TYAVSWFK..ELNLV.GL.Q.S
Retrocopy TITFSCFICIGQVV<FVLGGIFNVFWLMKFERFVFG<IGGECSAVAQDTYAVSWFKDQELNLVSGLQQFS

Parental  MARIGSTVNMNLMGWLYSKIEALLGSAGHTTLGITLMIGGITCILSLICALALAYLDQRAERILHKEQ
          MARIGS.V.MN.M.WLYSKIEA..GSAG.TT.G.TL.IGGI.CILSLICAL....L..R.ERILHKEQ
Retrocopy MARIGSIVDMNFMSWLYSKIEASWGSAGPTTPGVTLQIGGIKCILSLICALLGSRL-LRSERILHKEQ

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	4.81 RPM
SRP007412_cerebellum	0.12 RPM	3.65 RPM
SRP007412_heart	0.03 RPM	2.62 RPM
SRP007412_kidney	0.03 RPM	9.65 RPM
SRP007412_liver	0.00 RPM	6.76 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1427 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1427 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1427 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009263	1 retrocopy	retro_btau_1323,
Dasypus novemcinctus	ENSDNOG00000005048	1 retrocopy	retro_dnov_1121,
Macaca mulatta	ENSMMUG00000023510	1 retrocopy	retro_mmul_1210,
Oryctolagus cuniculus	ENSOCUG00000001272	1 retrocopy	retro_ocun_1528,
Pongo abelii	ENSPPYG00000014247	1 retrocopy	retro_pabe_1427 ,
Tupaia belangeri	ENSTBEG00000013974	1 retrocopy	retro_tbel_1396,
Tursiops truncatus	ENSTTRG00000002207	2 retrocopies	retro_ttru_1119, retro_ttru_1271,
Drosophila melanogaster	FBgn0031636	1 retrocopy	retro_dmel_45,