RetrogeneDB ID: retro_pabe_3319

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 8:40441409..40441803(-)
• Located in intron of: ENSPPYG00000018538

Retrocopy information

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

Parental gene information

• Parental gene symbol: NFYB
• Ensembl ID: ENSPPYG00000004892
• Aliases: None
• Description: nuclear transcription factor Y, beta [Source:HGNC Symbol;Acc:7805]

Sequence

>retro_pabe_3319
TCAAAAGAAAGTTGCAGAGAACAAAACATACATTTTTTGATTGCACATGTCACTAGGATAATGAAACATGCCATATCTCA
AATGGGAAATGCCCAAGAAAGTGTTAAAGAATGTGTACGTGTGTTCATCAGCTTTATAACCCCCGAGGCAAGTGAAAGAT
GCCTCCAAGAGAAATGGAAATGGCCAGTGGAGAGGATCTTCTCTTTGCCATGTCTACCATAGGCTTTGACAGTTATGTGG
AACCTCTAAAATTATCCCTCAAAAACTCAGAAAGTCTGTGAAAGGAGAGAAGGGAATTGGTGGAGAAGTCAGAGCTACAG
ATGGGCTAAGTGAAGAGCTTACAGAATAGGCATTTGCTAGCCAGTCACCAGCCGGCTTCATACCTGCTGCTGGG

Alignment

ORF - retro_pabe_3319 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.39 %
• Parental protein coverage: 65.7 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SKESFREQDIYLPIANVARIMKNAIPQTGKIAKDAKECVQECVSEFISFITSEASERCHQEKRK-TINGE
          SKES.REQ.I...IA.V.RIMK.AI.Q.G.....A.E.V.ECV..FISFIT.EASERC.QEK.K....GE
Retrocopy SKESCREQNIHFLIAHVTRIMKHAISQMG----NAQESVKECVRVFISFITPEASERCLQEKWK<MASGE

Parental  DILFAMSTLGFDSYVEPLKLYL-QKFREAMKGEKGIGGAVTATDGLSEELTEEAFTNQLPAGLITTDG
          D.LFAMST.GFDSYVEPLKL.L.QK.R...KGEKGIGG.V.ATDGLSEELTE.AF..Q.PAG.I...G
Retrocopy DLLFAMSTIGFDSYVEPLKLSL<QKLRKSVKGEKGIGGEVRATDGLSEELTE*AFASQSPAGFIPAAG

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	10.23 RPM
SRP007412_cerebellum	0.00 RPM	16.66 RPM
SRP007412_heart	0.00 RPM	9.12 RPM
SRP007412_kidney	0.03 RPM	12.93 RPM
SRP007412_liver	0.00 RPM	7.68 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3319 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3319 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3319 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014610	1 retrocopy	retro_cjac_1133,
Cavia porcellus	ENSCPOG00000003213	1 retrocopy	retro_cpor_901,
Dasypus novemcinctus	ENSDNOG00000009984	3 retrocopies	retro_dnov_1536, retro_dnov_758, retro_dnov_855,
Felis catus	ENSFCAG00000026471	1 retrocopy	retro_fcat_207,
Myotis lucifugus	ENSMLUG00000005468	1 retrocopy	retro_mluc_1764,
Ochotona princeps	ENSOPRG00000008117	2 retrocopies	retro_opri_36, retro_opri_657,
Pongo abelii	ENSPPYG00000004892	3 retrocopies	retro_pabe_2201, retro_pabe_2803, retro_pabe_3319 ,