RetrogeneDB ID: retro_pabe_3671

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: X:88152005..88152587(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AGPAT5
• Ensembl ID: ENSPPYG00000018320
• Aliases: None
• Description: 1-acyl-sn-glycerol-3-phosphate acyltransferase epsilon [Source:RefSeq peptide;Acc:NP_001124637]

Sequence

>retro_pabe_3671
CTAAAAGAAAGTGCCAAATTTATTGAAAAAGAAATGAGAAACAAGTGGCAGAGCTACATGAATGCGGAAACTGCTATGCA
TTTTATGATTTTTTTCCAGAAGGTACAAGGTATAACACCAGACAAACAAGTCCTTTCAGCTCGTCAGTTTGCTGCTCAAC
AAGGCCTTGCAGTATTAAAACATGCTGACACCACTAATAAAGACAGCTCATGTTACTTTTAATTCTGTGAAGAATTAGTT
GATGCAATTTATAATGTTACAGTAGTTTATGAAGGAAAAGATAAGGAGAAACTCAAAAATCACTATCCATGACTGAATTT
CTCTGCAAAGAATGCCTCAAAATTATTATTCACATTGATGATACAGACAAAAAACGTGTCCCAGAAGAGCAAGAATATAT
GAGAGGATGACTTCATGAACATTTTGAAATAAAAAAATAAGGTTTCAAAGAACTATGACTCACCAGACCCAGAAAGAAGA
AACAAATTTCTTAGAAAAACTGTTAATTTTGAATTAAGAATCAAGAAGACTTTAGCATCAGTATTCATCTTAAATGGTTT
GACTGATGGCATGCTTATGACC

Alignment

ORF - retro_pabe_3671 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51. %
• Parental protein coverage: 65.13 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VKRSAKFNEKEMRNKLQSYVDTGTPMYLVIFPEGTRYNPEQTKVLSASQAFAAQRGLAVLKHVLTPRIKA
          .K.SAKF.EKEMRNK.QSY....T.M...IF............VLSA.Q.FAAQ.GLAVLKH..T...K.
Retrocopy LKESAKFIEKEMRNKWQSYMNAETAMHFMIFFQKVQGITPDKQVLSARQ-FAAQQGLAVLKHADTTN-KD

Parental  THVAFDCMKNYLDAIYDVTVVYEGKDDGGQRRESPTMTEFLCKECPK-IHIHIDRIDKKDVPEEQEHMRR
          ....F.......DAIY.VTVVYEGKD........P....F..K...K.I.IHID..DKK.VPEEQE.MR.
Retrocopy SSCYF*FCEELVDAIYNVTVVYEGKDKEKLKNHYP*L-NFSAKNASK<IIIHIDDTDKKRVPEEQEYMRG

Parental  WLHERFEI-KDKMLIEFYESPDPERRKRFPGKSVNSKLSIKKTLPSMLILSGLTAGMLMT
          .LHE.FEI.K.K............R.K.F..K.VN..L.IKKTL.S..IL.GLT.GMLMT
Retrocopy *LHEHFEI>KNKVSKNYDSPDPERRNK-FLRKTVNFELRIKKTLASVFILNGLTDGMLMT

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	25.99 RPM
SRP007412_cerebellum	0.00 RPM	26.39 RPM
SRP007412_heart	0.00 RPM	6.11 RPM
SRP007412_kidney	0.00 RPM	20.29 RPM
SRP007412_liver	0.00 RPM	11.81 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3671 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3671 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3671 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005142	1 retrocopy	retro_chof_376,
Dasypus novemcinctus	ENSDNOG00000004979	1 retrocopy	retro_dnov_823,
Otolemur garnettii	ENSOGAG00000008958	1 retrocopy	retro_ogar_3477,
Pongo abelii	ENSPPYG00000018320	1 retrocopy	retro_pabe_3671 ,
Sarcophilus harrisii	ENSSHAG00000000051	1 retrocopy	retro_shar_687,
Tupaia belangeri	ENSTBEG00000013084	1 retrocopy	retro_tbel_2948,