RetrogeneDB ID: retro_pabe_2725

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 5:38449415..38450581(-)
• Located in intron of: ENSPPYG00000015408

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPPYG00000018452
• Aliases: None
• Description: None

Sequence

>retro_pabe_2725
ATGAGGCGGGTGACCCTGTTCCTAAACGGCAGCCCCAAGAACGGAAAGGTGGTTGCTGTATATGGAACTTTATCTGATTT
GCTTTCTGTGGCCAGCAGTAAACTCGGCATAAAAGCCACCAGTGTGTATAATGAGAAAGGTGGACTGATTGATAATATTG
CTTTGATCAGGGATGATGATGTTTTATTTGTGTGTGAGGGAGAGCCATTTATTGATCTTCAGACAGATTCTAAGCCTCCT
GAAGGATTGTTAGGATTCCACACAGAATGGCTAACATTAAATGTTGGAGGGAGGTATTTTACAACTACACGGAGCACTTT
AGTGAATAAAGAACCTGACAGTATGCTGGCCCACATGCTTAAGGACAGAGGTGTCTGGGGAAATAAGCAAGATCATAGAG
GAGCTTTCTTAATTGACCAAAGTCCTGAGTACTTTGAACCCACTTTGAACTACTGTGTCATGGACAGCTCATTGTAAATG
ATGGCATTAATTTATTGGGTGTGTTAGAAGAAGCAAGATTTTTTGGTATTGACTCACTGATTGAACACCTAGAACTGGCA
ATAAAGAATTCTCAACCACCAGAGGATCATTCACCAATATCTTGAAAGGAATTTGTCCGATTTTTGCCAGCAACTCCAAC
CAAGTCAGAACTGTGATGCCAGAGTTTGAACTTCAGTGGTGCTGATCTTTCTCGTTAGGACCTTCAACACATTAACTTCA
AAATGGCCAATTTAAGCCGCTGCAATCTTGCACATGCAAATCTTTACTGTGCAAATCTTGAATGAGCTGATCTCTCTGGA
CCAGTGCTAGACTGTGCAAATCTCCAGGGAGTCAAGATGCTCTGTTCTAATGCAGAAGGAGCATCCCTGAAACTGTGTAA
TTTTGAGGATCCTTCTGGTCTTAAAGCCAGTTTAGAAGGTGCTAATCTGAAAGGTGTGGATATGGAAGGAAGTCAGATGA
CAGGAATTAACCTGAGAGTGGCTACCTTAAAAAATGCAAAGTTGAAGAACTGTAACCTCAGAGGAGCAACTCTGGCAGGA
ACCGATTTAGAGAACTGTGATCTGTCTGGGTGTGATCTTCAAGAAGCCAACTTGAGAGGGTCCAACGTGAAGGGAGCTAT
ATTTGAAGAGATGCTGACACCACTATACATGTTGCAAAATGTCAGA

Alignment

ORF - retro_pabe_2725 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.59 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MRRVTLFLNGSPKNGKVVAVYGTLSDLLSVASSKLGIKATSVYNGKGGLIDDIALIRDDDVLFVCEGEPF
          MRRVTLFLNGSPKNGKVVAVYGTLSDLLSVASSKLGIKATSVYN.KGGLID.IALIRDDDVLFVCEGEPF
Retrocopy MRRVTLFLNGSPKNGKVVAVYGTLSDLLSVASSKLGIKATSVYNEKGGLIDNIALIRDDDVLFVCEGEPF

Parental  IDPQTDSKPPEGLLGFHTDWLTLNVGGRYFTTTRSTLVNKEPDSMLAHMFKDKGVWGNKQDHRGAFLIDR
          ID.QTDSKPPEGLLGFHT.WLTLNVGGRYFTTTRSTLVNKEPDSMLAHM.KD.GVWGNKQDHRGAFLID.
Retrocopy IDLQTDSKPPEGLLGFHTEWLTLNVGGRYFTTTRSTLVNKEPDSMLAHMLKDRGVWGNKQDHRGAFLIDQ

Parental  SPEYFEPILNY-LRHGQLIVNDGINLLGVLEEARFFGIDSLIEHLEVAIKNSQPPEDHSPISRKEFVRFL
          SPEYFEP.LNY.L.HGQLIVNDGINLLGVLEEARFFGIDSLIEHLE.AIKNSQPPEDHSPIS.KEFVRFL
Retrocopy SPEYFEPTLNY<LCHGQLIVNDGINLLGVLEEARFFGIDSLIEHLELAIKNSQPPEDHSPIS*KEFVRFL

Parental  LATPTKSELRCQGLNFSGADLSRLDLRYINFKMANLSRCNLAHANLCCANLERADLSGSVLDCANLQGVK
          .ATPTKSEL.CQ.LNFSGADLSR.DL..INFKMANLSRCNLAHANL.CANLE.ADLSG.VLDCANLQGVK
Retrocopy PATPTKSEL*CQSLNFSGADLSR*DLQHINFKMANLSRCNLAHANLYCANLE*ADLSGPVLDCANLQGVK

Parental  MLCSNAEGASLKLCNFEDPSGLKANLEGANLKGVDMEGSQMTGINLRVATLKNAKLKNCNLRGATLAGTD
          MLCSNAEGASLKLCNFEDPSGLKA.LEGANLKGVDMEGSQMTGINLRVATLKNAKLKNCNLRGATLAGTD
Retrocopy MLCSNAEGASLKLCNFEDPSGLKASLEGANLKGVDMEGSQMTGINLRVATLKNAKLKNCNLRGATLAGTD

Parental  LENCDLSGCDLQEANLRGSNVKGAIFEEMLTPLHMSQSVR
          LENCDLSGCDLQEANLRGSNVKGAIFEEMLTPL.M.Q.VR
Retrocopy LENCDLSGCDLQEANLRGSNVKGAIFEEMLTPLYMLQNVR

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	5.58 RPM
SRP007412_cerebellum	0.12 RPM	11.19 RPM
SRP007412_heart	0.00 RPM	14.33 RPM
SRP007412_kidney	0.00 RPM	10.61 RPM
SRP007412_liver	0.00 RPM	5.57 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2725 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2725 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2725 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3305
Pan troglodytes	retro_ptro_2166
Gorilla gorilla	retro_ggor_1309

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012157	1 retrocopy	retro_chof_323,
Gorilla gorilla	ENSGGOG00000004480	3 retrocopies	retro_ggor_1309, retro_ggor_2264, retro_ggor_2791,
Macaca mulatta	ENSMMUG00000010151	3 retrocopies	retro_mmul_1083, retro_mmul_1218, retro_mmul_2072,
Nomascus leucogenys	ENSNLEG00000016156	3 retrocopies	retro_nleu_1386, retro_nleu_2499, retro_nleu_2990,
Pongo abelii	ENSPPYG00000008616	1 retrocopy	retro_pabe_2093,
Pongo abelii	ENSPPYG00000018452	3 retrocopies	retro_pabe_1527, retro_pabe_2725 , retro_pabe_3457,