RetrogeneDB ID: retro_pabe_1037

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 13:23905432..23905884(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPPYG00000019046
• Aliases: None
• Description: None

Sequence

>retro_pabe_1037
GATGTCTACGGCAACACTGCTCTCCACTATGCTGTCCTATAATGAGAGTACATTCCTGGTAGAAAAACTACTTTCCTATG
ATACGGATATTGAAGTGCTGAACAACGATGGACACATACCACTTTTACTTGCCGCAGTTTGCAAAAGACAGCAAATGCTG
GAATTTTTAGTGAAGAAACAAGCAAATGCACATGCTGTTGATAGGTTGAGAGGAACAGCCTTCACGCCTGCCGTACATTA
TGGCTCGTTAGGTATAGTCGGCATTCTTCAACAAAATATTACTGTCTTTATTCAAGATACGTATGGACAGACAGCAAACG
ATTATGCTATTTGTGGTGTTTTGACTAGCATTCAACAACAAATTTTGCAACATAAAAAAAAAGATACCTGAAAATGGTCT
TCAAAATGACAATCCAGAAGCATCAAAAGAATGCAAGTTTGAAAAAAGGAGG

Alignment

ORF - retro_pabe_1037 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.13 %
• Parental protein coverage: 51.69 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DIYGNTALHYAV-YNEGTSLAEKLLSCHANIEALNEEGNTPLLFAINSRRQQMVEFLLNNQANVHAVDNF
          D.YGNTALHYAV.YNE.T.L.EKLLS....IE.LN..G..PLL.A....RQQM.EFL...QAN.HAVD..
Retrocopy DVYGNTALHYAV>YNESTFLVEKLLSYDTDIEVLNNDGHIPLLLAAVCKRQQMLEFLVKKQANAHAVDRL

Parental  RRTALMLAVQHNSSSIVNLLLQQNINIFSQDLFGQTAEDYAVCCNFRSIQQQILEH-KNKILKNHLRNDN
          R.TA...AV...S..IV..L.QQNI..F.QD..GQTA.DYA.C....SIQQQIL.H....I..N.L.NDN
Retrocopy RGTAFTPAVHYGSLGIVGIL-QQNITVFIQDTYGQTANDYAICGVLTSIQQQILQH>XXXIPENGLQNDN

Parental  QETAAMKPGSLKKRK
          .E..A.K.....KR.
Retrocopy PE--ASKECKFEKRR

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	4.53 RPM	2.88 RPM
SRP007412_cerebellum	1.22 RPM	0.97 RPM
SRP007412_heart	2.56 RPM	0.00 RPM
SRP007412_kidney	1.09 RPM	0.07 RPM
SRP007412_liver	0.86 RPM	0.03 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1037 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1037 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1037 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000008211	2 retrocopies	retro_cjac_2331, retro_cjac_2672,
Microcebus murinus	ENSMICG00000017899	2 retrocopies	retro_mmur_1151, retro_mmur_246,
Macaca mulatta	ENSMMUG00000008983	1 retrocopy	retro_mmul_1761,
Pongo abelii	ENSPPYG00000019046	1 retrocopy	retro_pabe_1037 ,
Tupaia belangeri	ENSTBEG00000017150	1 retrocopy	retro_tbel_490,