RetrogeneDB ID: retro_pabe_3222

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 7_random:7729636..7730447(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SAPCD2
• Ensembl ID: ENSPPYG00000019804
• Aliases: None
• Description: suppressor APC domain containing 2 [Source:HGNC Symbol;Acc:28055]

Sequence

>retro_pabe_3222
CTGCTGTTCGCGCCAGCCGACGAGCCGCGAATGGTCCTGGAGAGGAAGCCCCTGCCCCTGGGCGAGCGCGCTTCTCTGGC
CGGTCCCAGCCGCGCGGCCGGCAGCCCAGAGCAGCTGTGCGACCCCGCCGAAGCGGTGCACTGCCCCGTGGAACCAGAGC
GGTCCCAGAGCGCGGCGCTGGAACAGAGCCCCAGCGCGGACGCAGGTGCAGCGGCCTGCAGGGCTTTGGAGGCAGACTCA
GGGGATGCGCCGCGGGCCCCCAGTGCCCGAGGAGAACGTCAGAGGCACACCATCACCAGCGGCGTGGACTGCGGCCTGCT
GAAGCAGATGAAGGAGCTGAAGCAGGAGAAGGAGGTGCTGCTGCAGGATTTGGAGATGATGCCGCGGGGCCGTGATTGGT
ACCAGCAGCAGCTGCAACGAGTGCAGGAGCGCCAGTGCCGCCTGGGCCAGAGCAGAGCCAGCGTCGACTTTGGGGCCACG
GGGAGCCCCCGCCCACTGGGGCGGCTACTGTCCAAGGTACAGGAGGTGACCGGCTGCCTGGGGGAGCTGCTGGCTGCGGC
CTGTGCCAGCTGGCCCTGCCCACGTCCTCCTCGGGGCCCCGTGCTCTGCCCTAAGGTCAACCTCGTCCCCGGACTGTCAG
CAGCAGACCATCCTCATGCTGAAGGAGCAGAGCTGACTCCTTACCCGGGAGGTGACCGAGAAGAGTGAGCGCATCACGCA
GCTGGAGCAGAAGTCAGCGCTCATTAAGCAGCTGTTTGAGGCCCTCGCCCTGAGCCAGCAGGACGGGGGGCCTCTGGACC
CCACCTTCATC

Alignment

ORF - retro_pabe_3222 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.83 %
• Parental protein coverage: 69.39 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LVFAPADEPRTVLERKPLPLGVRAPLAGPSGAARSPEQLCAPAEAAPCPAEPERSQSAALEPSSSADAGA
          L.FAPADEPR.VLERKPLPLG.RA.LAGPS.AA.SPEQLC.PAEA..CP.EPERSQSAALE.S.SADAGA
Retrocopy LLFAPADEPRMVLERKPLPLGERASLAGPSRAAGSPEQLCDPAEAVHCPVEPERSQSAALEQSPSADAGA

Parental  VACRALEADSGDARRAPRARGERRRHTITSGVDCGLLKQMKELEQEKEVLLQGLEMMARGRDWYQQQLQR
          .ACRALEADSGDA.RAP.ARGER.RHTITSGVDCG..................LEMM.RGRDWYQQQLQR
Retrocopy AACRALEADSGDAPRAPSARGERQRHTITSGVDCGXXXXXXXXXXXXXXXXXXLEMMPRGRDWYQQQLQR

Parental  VQERQRHLGQSRASADFGAAGSPRPLGRLLPKVQEVARCLGELLAAACAS-RALPPSSSGP-PCPALTST
          VQERQ..LGQSRAS.DFGA.GSPRPLGRLL.KVQEV..CLGELLAAACAS..ALP.SSSGP.PC.AL.ST
Retrocopy VQERQCRLGQSRASVDFGATGSPRPLGRLLSKVQEVTGCLGELLAAACAS<LALPTSSSGP<PCSALRST

Parental  SPRGWQQQTILMLKEQNRLLTQEVTEKSERITQLEQEKSALIKQLFEARALSQQDGGPLDSTFI
          S....QQQTILMLKEQ..LLT.EVTEKSERITQLEQ.KSALIKQLFEA.ALSQQDGGPLD.TFI
Retrocopy SSPDCQQQTILMLKEQS*LLTREVTEKSERITQLEQ-KSALIKQLFEALALSQQDGGPLDPTFI

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	0.50 RPM	0.28 RPM
SRP007412_cerebellum	0.36 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.03 RPM	0.66 RPM
SRP007412_liver	0.00 RPM	0.12 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3222 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3222 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3222 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000186193	2 retrocopies	retro_hsap_3734, retro_hsap_3738,
Macaca mulatta	ENSMMUG00000007112	1 retrocopy	retro_mmul_1682,
Nomascus leucogenys	ENSNLEG00000008908	2 retrocopies	retro_nleu_2867, retro_nleu_2939,
Pongo abelii	ENSPPYG00000019804	5 retrocopies	retro_pabe_3124, retro_pabe_3222 , retro_pabe_3223, retro_pabe_3233, retro_pabe_3527,
Pan troglodytes	ENSPTRG00000021589	6 retrocopies	retro_ptro_2530, retro_ptro_2532, retro_ptro_2534, retro_ptro_2537, retro_ptro_2543, retro_ptro_2992,