RetrogeneDB ID: retro_pabe_419

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:96040355..96041252(-)
• Located in intron of: ENSPPYG00000000744

Retrocopy information

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

Parental gene information

• Parental gene symbol: PHB2
• Ensembl ID: ENSPPYG00000004214
• Aliases: None
• Description: prohibitin-2 [Source:RefSeq peptide;Acc:NP_001125603]

Sequence

>retro_pabe_419
ATGGCCCAGAACTTGAAGGACTTGGCGGGACGGCTGCCCGCCAGGCCCCGGGGCATGGGCACGGCCCTGAAGCTGTTGCT
GGGGGCCGGCACCGTGGCCTACGGTGTGCGCGAATCCGTGTTCACCGTGGAAGGCAGGCACAGAGCCATCTTCTTCAATC
GGATCGGTGGAGTGCAGCAGGACACTATGCTGGCCGAGGGCCTTCACTTCAGGATCCCTTGGTTCCAGTACCCCATTATC
TATGACATTCGGGCCAGACCTCAAAAAGCCTACTCCTCTACAGGCTCCAAAGACCTACAGATGGTGAATATCTCCCTGTG
AGTGTTGTCTCGACCCAATGCTCAGGAGCTTCCTAGCATGTACCAGCGCCTAAGGCTGGACTACGAGGAACGAGTGTTGC
CGTCCATTGTCAACGAGGTGCTCAAGAGTGTGGTGGCCAAGTTCAATGCCTCACAGCTGATCACCCAGTGGGCCCAGGTA
TCCCTGTTGATCCGCCGGGAGCTGACAGAGAGGGCCAAGGACTTCAGCCTCATCCTGGATGATGTGGCCATCACAGAGCT
GAGCTTTAGCCGAGAGCACACAGCTGCTGTAGAAGCCAAACAAGTGGCCCAGCAGGAGGCCCAGCGGGCCCAATTCTTGG
TAGAAAAGGCGAAGCAGGAACAGCGGCAGAAGATTGTACAGGCCGAGGGTGAGGCCGAGGCTGCCAAGATGCTTGGAGAA
GCACTGAGCAAGAACCCCGGCTACATCAAACTTTGCAAGATTCGAGCAGCCCAGAATATCTCCAAGACGATAGCCACATC
ATAGAATCGTATCTATCTCACGGCTGACAACCTTGTGCTGAACTTACAGGATGAAAGTTTCACCGGAGGAAGTGACAGCC
TCATCAAGGGTAAGAAA

Alignment

ORF - retro_pabe_419 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.98 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAQNLKDLAGRLPAGPRGMGTALKLLLGAGAVAYGVRESVFTVEGGHRAIFFNRIGGVQQDTILAEGLHF
          MAQNLKDLAGRLPA.PRGMGTALKLLLGAG.VAYGVRESVFTVEG.HRAIFFNRIGGVQQDT.LAEGLHF
Retrocopy MAQNLKDLAGRLPARPRGMGTALKLLLGAGTVAYGVRESVFTVEGRHRAIFFNRIGGVQQDTMLAEGLHF

Parental  RIPWFQYPIIYDIRARPRKISSPTGSKDLQMVNISLRVLSRPNAQELPSMYQRLGLDYEERVLPSIVNEV
          RIPWFQYPIIYDIRARP.K..S.TGSKDLQMVNISL.VLSRPNAQELPSMYQRL.LDYEERVLPSIVNEV
Retrocopy RIPWFQYPIIYDIRARPQKAYSSTGSKDLQMVNISL*VLSRPNAQELPSMYQRLRLDYEERVLPSIVNEV

Parental  LKSVVAKFNASQLITQRAQVSLLIRRELTERAKDFSLILDDVAITELSFSREYTAAVEAKQVAQQEAQRA
          LKSVVAKFNASQLITQ.AQVSLLIRRELTERAKDFSLILDDVAITELSFSRE.TAAVEAKQVAQQEAQRA
Retrocopy LKSVVAKFNASQLITQWAQVSLLIRRELTERAKDFSLILDDVAITELSFSREHTAAVEAKQVAQQEAQRA

Parental  QFLVEKAKQEQRQKIVQAEGEAEAAKMLGEALSKNPGYIKLRKIRAAQNISKTIATSQNRIYLTADNLVL
          QFLVEKAKQEQRQKIVQAEGEAEAAKMLGEALSKNPGYIKL.KIRAAQNISKTIATS.NRIYLTADNLVL
Retrocopy QFLVEKAKQEQRQKIVQAEGEAEAAKMLGEALSKNPGYIKLCKIRAAQNISKTIATS*NRIYLTADNLVL

Parental  NLQDESFTRGSDSLIKGKK
          NLQDESFT.GSDSLIKGKK
Retrocopy NLQDESFTGGSDSLIKGKK

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	44.73 RPM
SRP007412_cerebellum	0.12 RPM	40.25 RPM
SRP007412_heart	0.03 RPM	40.49 RPM
SRP007412_kidney	0.20 RPM	85.25 RPM
SRP007412_liver	0.24 RPM	86.79 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_419 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_419 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_419 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013760	1 retrocopy	retro_amel_1928,
Canis familiaris	ENSCAFG00000014439	1 retrocopy	retro_cfam_1885,
Callithrix jacchus	ENSCJAG00000007137	1 retrocopy	retro_cjac_781,
Homo sapiens	ENSG00000215021	1 retrocopy	retro_hsap_624,
Gorilla gorilla	ENSGGOG00000004281	1 retrocopy	retro_ggor_547,
Macaca mulatta	ENSMMUG00000010205	2 retrocopies	retro_mmul_2599, retro_mmul_2623,
Nomascus leucogenys	ENSNLEG00000005021	2 retrocopies	retro_nleu_121, retro_nleu_450,
Pongo abelii	ENSPPYG00000004214	3 retrocopies	retro_pabe_419 , retro_pabe_557, retro_pabe_559,
Rattus norvegicus	ENSRNOG00000012999	1 retrocopy	retro_rnor_2373,