RetrogeneDB ID: retro_pabe_2803

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 5:178297898..178298314(-)
• Located in intron of: ENSPPYG00000016063

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_2803
GATAGGGACAGTGCTAGGACAGAGGCTTCTCGACTCCGGATTTCTGCAGACTGCGCTGGAGGAAGTCATGCTGCACAGCC
TTGTGCTGACACTGGGAACAGTGTGAATAATCATGAAACCACAGATGCTTCAAAAGAAAGTTTTGGAGAACAAGATATCT
GCGTTCCCACTGCAGATGCGGCAAGGATCATGAAGAATGTCCCTCAGAGGGACAGACTGCACAGGATGCCAAAGAATGTG
TTCCAGAGTGTGTGGGTTCATCAGCTTCACGGCACCTGAAGCAAGTGAAAGATGCCTGGGAGACTGAGGCGACAGTCAGT
GGGGAGGGTGCTCTCTTTGCCCTGTTCACCTGAGGCTTTCAGAGTTATGCAGAAGCGCTGGGGTGGTGCCTTCAGGCACT
CAGAGAGGCTAGGAGA

Alignment

ORF - retro_pabe_2803 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.39 %
• Parental protein coverage: 69.08 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DGDSSTTDASQLGISADYIGGSHYVIQPHDDTEDSMNDHEDTNGSKESFREQDIYLPIANVARIMKNAIP
          D.DS..T.AS.L.ISAD..GGSH...QP..DT..S.N.HE.T..SKESF.EQDI..P.A..ARIMKN..P
Retrocopy DRDSARTEASRLRISADCAGGSH-AAQPCADTGNSVNNHETTDASKESFGEQDICVPTADAARIMKN-VP

Parental  Q-TGKIAKDAKECVQECVSEFISFITSEASERCHQEKRKTINGEDILFAMSTLGFDSYVEPLKLYLQKFR
          Q..G..A.DAKECV.ECV....S............E...T..GE..LFA..T.GF.SY.E.L...LQ..R
Retrocopy Q<EGQTAQDAKECVPECVGSSASRHLKQVKDAWETE--ATVSGEGALFALFT*GFQSYAEALGWCLQALR

Parental  EAMK
          EA..
Retrocopy EARR

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	0.00 RPM	12.93 RPM
SRP007412_liver	0.37 RPM	7.68 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2803 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2803 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2803 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Macaca mulatta	retro_mmul_2119

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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,