RetrogeneDB ID: retro_pabe_3242

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 8:1565600..1566257(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DFFA
• Ensembl ID: ENSPPYG00000001899
• Aliases: None
• Description: DNA fragmentation factor subunit alpha [Source:RefSeq peptide;Acc:NP_001126304]

Sequence

>retro_pabe_3242
ATGGAGGTGACTGGGGACACCAGGGCATCAGAACCCGGCGAGATTCGGACTCTAAAGCTGGGCCGGCTGCACTGCAACTA
CAGCCGTGAACAGCACAGGTGGCCACCTCCTGCCTCGAGGACCTGAACAGCAAGGCCTGTGACAGCCCGGCCATTGACAA
GTCCCTGCCACTGATCACCCTGGTCCTGCAGAGGCTGGCACAATGGTGATGAGGATTACTTCCTGTGTCTGCCTTCCAAT
ACTAAGTGTTTGGCATTGACCAATAATGAGACGAGGACATAGGACAATTCTGATGGAGATACGGCTAGGGTTTCCCAGGC
ATCCTTTCATGTGGATGAACTATAGCGGGGCGTGGCTGAAGTGGAAGAATGTGGCCAGGCACCTGAACAAGGCTCCATCC
AGTGCCATCCTCCTATCAGAGGAAGACCGTCCCGTGCTCATTCATATTCCGTGTTCAGACCTGGCTCAGGAACTAAGCCA
AGGCTGTGCCACCATCCAGGGCCACAGAACGCACTCCAGCAGGTGCTTGGCAGGGGAAGCGGTCTGTCCGGGCAGCTCCT
GGAGCTGTACCTCCAGGTTTTGGAGAAAGAGGGCAGCCTCTTGTCAAAGCAAGAGGAATCTAAAGCAGCTTTCGGTGATG
AGGCAGAGGCAGTAGAC

Alignment

ORF - retro_pabe_3242 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.52 %
• Parental protein coverage: 67.67 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  MEVTGEAGVPESGEIRTLKPCLLRRNYSREQHG-VAASCLEDLRSKACDILAIDKSLTPVTLVL-AEDGT
          MEVTG.....E.GEIRTLK...L..NYSREQH..VA.SCLEDL.SKACD..AIDKSL...TLVL.AE.GT
Retrocopy MEVTGDTRASEPGEIRTLKLGRLHCNYSREQHR<VATSCLEDLNSKACDSPAIDKSLPLITLVL<AEAGT

Parental  IV-DDDDYFLCLPSNTKFVALANNEKWAYNNSDGGTAWISQESFDVDE-TDSGAG-LKWKNVARQLKEDL
          .V.D..DYFLCLPSNTK..AL.NNE.....NSDG.TA..SQ.SF.VDE.T..G.G.LKWKNVAR.L....
Retrocopy MV<DE-DYFLCLPSNTKCLALTNNETRT*DNSDGDTARVSQASFHVDE<TIAGRG<LKWKNVARHLNKAP

Parental  SSIILLSEEDLQMLVDAPCSDLAQELHQSCATVQ-RLQHTLQQVLDQREEVRQSKQLLQLYLQALEKEGS
          SS.ILLSEED...L...PCSDLAQEL.Q.CAT.Q...Q..LQQVL........S.QLL.LYLQ.LEKEGS
Retrocopy SSAILLSEEDRPVLIHIPCSDLAQELSQGCATIQ<GPQNALQQVLGRGSGL--SGQLLELYLQVLEKEGS

Parental  LLSKQEESKAAFGEEADAVD
          LLSKQEESKAAFG.EA.AVD
Retrocopy LLSKQEESKAAFGDEAEAVD

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	12.22 RPM
SRP007412_cerebellum	0.00 RPM	7.30 RPM
SRP007412_heart	0.00 RPM	8.58 RPM
SRP007412_kidney	0.00 RPM	18.26 RPM
SRP007412_liver	0.00 RPM	8.45 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3242 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3242 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3242 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3926
Gorilla gorilla	retro_ggor_2642

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000013535	1 retrocopy	retro_btau_211,
Homo sapiens	ENSG00000160049	1 retrocopy	retro_hsap_3926,
Gorilla gorilla	ENSGGOG00000012721	1 retrocopy	retro_ggor_2642,
Pongo abelii	ENSPPYG00000001899	1 retrocopy	retro_pabe_3242 ,