RetrogeneDB ID: retro_pabe_2521

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 4:63406709..63409767(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPPYG00000014750
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: GLDC
• Ensembl ID: ENSPPYG00000019225
• Aliases: None
• Description: glycine dehydrogenase (decarboxylating) [Source:HGNC Symbol;Acc:4313]

Sequence

>retro_pabe_2521
ATGCAGTCCTGTGCCAGGGCGTGGGGGCTGCGCCTGGGCGGCGGAGTCGGGGGCGGCCGCCGCCTGGCTGGGGGATCGGG
GCTGTGCTGGGCGCCGCGGGCCGGGACAGCAGCAGTGGCGGCGGGGATAGCGCCGCGGCTGGGGCCTTGCGCCTCCTGGA
GCGCCTTCTGCCCAGACAAGACGACTTCGCTCGGAGGCACACCGGCCCTGGGGACAAAGACCAGAGAGAGATGCTGCAGA
CCTTGGGGCTGGCGAGCATTGATGAATTGATCGAGAAGACGGTCCCTGCCAACATCCGTTTGAAAAGACCCTTGAAAATG
GAAGACCCTGTTTGTGAAAATGAAATCCTTGCAACTCTGCATGCCATTTCAAGCAAAAACCAGATCTGGAGATCGTATAT
TGGCATGGGCCATTGTAACTGCTCAGTGCCACAGACGATTTTCCGGAACTTACTGGAGAACTCAGAATGGATCACCCAGT
ATACTCCATACCAGCCTGAGGTGTCTCAGGGGAGACTGGAGAGTTTACTCAACTACCAGACCATGGTGTGTGACATCACA
GGCCTGGACATGGCCAATGCATCCCTGCTGGATGAGGGGACTGCAGCTGCAGAGGCACTGCAGCTGTGCTACAGACACAA
CAAGAGGAGGAAATTTTTTGTTGACCCCTGTTGCCACCCACAGACAATAGCTGTTGTCCAGACTGGAGCCAAATATACTG
GAGTCCTCATTGAGCTGAAGTTACCCTGTGAAATGGACTTCAGTAGAAAAGATGTCAGCGGAGTGTTGTTCCAGGACCCA
GACACGGAGGGGAAGGTGGAAGACTTTATGGAACTCGTGGAGAGAGCTCATCAGAGTGGGGGCCTGGCCTGCTGTGCTAC
TGACCTTTTAGCTTTGTGCATCTTGAGGCCACCTGGAGAATTTGGGGTAGACATCGCCCTGGGAAGCTCCCAGAGATTTG
GAGTGCCACTGGGCTATGGGGGACCCCATGCAGCATTTTTTGCTGTCCGAGAAAGCTTGGTGAGAATGATGCCTGGAAGA
ATGGTGGGGGTAACAAGAGATGCCACTGGGAAAGAAGTGTATCGTCTTGCTCTCCAAACCAGGGAGCAACACATTCGGAG
AGACAAGGCTACCAGCAACATCTGTACAGCTCAGGCCCTCTTGGTGAATATGGCAGCCATGTTTGCAATCTACCATGGTT
CCCATGGGCTGGAGCATATTGCTAGGAGGGTACACAATGCCACTTTGATTTTGTCAGAAGGTCTCAAGTGAGCAGGGCAT
CAACTCCAGCATGACCTGTTCTTTGATATCTTGAAGATTCAGTGTGGCTGCTCAGTGAAGGAGGTCTTGGGCAGGGCTGC
TCAGTGGCAGATCAATTTTCGGCTTTTTGAGGATGGCACACTTGGTATTTCTCTTGATGAAACAGTCAATGAAAAAGATC
TGGACGATTTGTTGTGGATCTTTGGTTGTGAGTCATCTGCAGAACTGGTTGCTGAAAGCATAGGAGAGGAGTGCAGAGGT
ATTCCAGGGTCTGTGTTCAAGAGGACCAGCCCGTTCCTCACCCATCAAGTGTTCAACAGCTACCACTCTGAAACAAATAT
TTTCCGGTATATGAAGAAACTGGAAAATAAAGACATTTCCCTTGTTCACAGCATGATTCCACTGGGATCCTGCACCATGA
AACTGAACAGTTCGTCTGAACTCGCACCTATGACATGGAAAGAATTTGCAAACATCTACCCCTTTGTGCCTCTGGACCAA
GCTCAAGGATATCAGCAGCTTTTCCGAGAGCTTGAGAAGGATTTGTGTGAACTCACAGGTTATGACCAGGTCTGTTTCCA
GCCAAACAGCGGAGCCCAGGGAGAATATGCTGGACTGGCCACTATCCGAGCCTACTTAAACCAGAAAGGAGAGAGGCACA
GAACGGTTTGCCTCATTCCAAAATCAGCACATGGGACCAACCCAGCAAGTGCCCACATAGCAGGCATGAAGATTCAGCCT
GTGGAGGTGGATAAATGTGGGAATATTGATGCAGTTCACCTCAAGGCCATGGTGGATAAGCACAAGGAGAACCTAGCAGC
CATCATGATTACATACCCATCCACCAATGGGGTGTTTGAAGAGAACATCAGTGACATGTGTGACCTCATCCATCAACATG
GAGGACAGGTCTACCTAGATGGGGCAAATATGAACGCTCAGGTGGGAATCTGTCACCCTGGAGACTTTGGGTCTGATGTC
TCGCACCTAAATCTTCACAAGACCTTCTGCTTTCCCCACGGAGGAGGTGGTCCTGGCATGGGGCCCATCGGAGTGAAGAA
ACATCTTGCCCCATTTTTGGCCAATCATCCCATCATTTCACTAAAGCGGAATGAGGATGCCTGTCCTGTGGGAACAGTCA
GTGAGGCCCCACGGGGCTCCAGTTCCATCTTGCCCATTTCCTGGGCTTATATCAAGATGATGGGAGGCAAGGGCTTAAAC
AAGCCACAGAAACTGCGATATTAAATGCCAACTACATGGCCAAGCGATTAGAAAAACACTACAGAATTCTTTTCAGGGGT
GCAAGAGGTTATGTGGGTCATGAATTTATTTTGGACACGAGACCCTTCAAAAAGTCTGCAAATATTGAGGCTGTGGATGT
GGCCAAGAGACTCCAGGATTATGGATTTCATGCCCCTACCGTGCCCTGGCCTGTGGCAGGGACCCTCATGGTTGAGCCCA
CTGAGTCGGAGGACAAGGCAGAGCTGGACAGTTTCTGTGATGCCATGATCAGCATTCGGCAGGAAATTGCTGACATTGAG
GAGGGCCGCATCGACCCCAGGGTCAATCCGCTGAAGATGTCTCCACACTCCCTGACCTGCATTACATCTTCCCACTGGGA
CCGACCTTATTCCAGAGAGGTGGCAGCATTCCCACTCCCCTTCGTGAAACCAGAGAACAAATTCTGGCCAATGATTGCCC
GGATTGATGACATATATGGAGATCAGCACCTGGTTTGTAACTGCCCACCCATGGAAGTTTATGAGTCTCCATTTTCTGAA
CAAAAGAGGGCCTCTTCT

Alignment

ORF - retro_pabe_2521 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.69 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MQSCARAWGLRLGRGVGGGRLLAGGSGPCWAPR-GRDSSSGGGDSAAAGASRLLERLLPRHDDFARRHIG
          MQSCARAWGLRLG.GVGGGR.LAGGSG.CWAPR.GRDSSSGGGDSAAAGA.RLLERLLPR.DDFARRH.G
Retrocopy MQSCARAWGLRLGGGVGGGRRLAGGSGLCWAPR<GRDSSSGGGDSAAAGALRLLERLLPRQDDFARRHTG

Parental  PGDKDQREMLQTLGLASIDELIEKTVPANIRLKRPLKMEDPVCENEILATLHAISSKNQIWRSYIGMGYY
          PGDKDQREMLQTLGLASIDELIEKTVPANIRLKRPLKMEDPVCENEILATLHAISSKNQIWRSYIGMG..
Retrocopy PGDKDQREMLQTLGLASIDELIEKTVPANIRLKRPLKMEDPVCENEILATLHAISSKNQIWRSYIGMGHC

Parental  NCSVPQTILRNLLENSGWITQYTPYQPEVSQGRLESLLNYQTMVCDITGLDMANASLLDEGTAAAEALQL
          NCSVPQTI.RNLLENS.WITQYTPYQPEVSQGRLESLLNYQTMVCDITGLDMANASLLDEGTAAAEALQL
Retrocopy NCSVPQTIFRNLLENSEWITQYTPYQPEVSQGRLESLLNYQTMVCDITGLDMANASLLDEGTAAAEALQL

Parental  CYRHNKRRKFFVDPRCHPQTIAVVQTRAKYTGVLTELKLPCEMDFSGKDVSGVLFQYPDTEGKVEDFTEL
          CYRHNKRRKFFVDP.CHPQTIAVVQT.AKYTGVL.ELKLPCEMDFS.KDVSGVLFQ.PDTEGKVEDF.EL
Retrocopy CYRHNKRRKFFVDPCCHPQTIAVVQTGAKYTGVLIELKLPCEMDFSRKDVSGVLFQDPDTEGKVEDFMEL

Parental  VERAHQSGSLACCATDLLALCILRPPGEFGVDIALGSSQRFGVPLGYGGPHAAFFAVRESLVRMMPGRMV
          VERAHQSG.LACCATDLLALCILRPPGEFGVDIALGSSQRFGVPLGYGGPHAAFFAVRESLVRMMPGRMV
Retrocopy VERAHQSGGLACCATDLLALCILRPPGEFGVDIALGSSQRFGVPLGYGGPHAAFFAVRESLVRMMPGRMV

Parental  GVTRDATGKEVYRLALQTREQHIRRDKATSNICTAQALLANMAAMFAIYHGSHGLEHIARRVHNATLILS
          GVTRDATGKEVYRLALQTREQHIRRDKATSNICTAQALL.NMAAMFAIYHGSHGLEHIARRVHNATLILS
Retrocopy GVTRDATGKEVYRLALQTREQHIRRDKATSNICTAQALLVNMAAMFAIYHGSHGLEHIARRVHNATLILS

Parental  EGLKRAGHQLQHDLFFDTLKIQCGCSVKEVLGRAAQRQINFRLFEDGTLGISLDETVNEKDLDDLLWIFG
          EGLK.AGHQLQHDLFFD.LKIQCGCSVKEVLGRAAQ.QINFRLFEDGTLGISLDETVNEKDLDDLLWIFG
Retrocopy EGLK*AGHQLQHDLFFDILKIQCGCSVKEVLGRAAQWQINFRLFEDGTLGISLDETVNEKDLDDLLWIFG

Parental  CESSAELVAESMGEECRGIPGSVFKRTSPFLTHQVFNSYHSETNIVRYMKKLENKDISLVHSMIPLGSCT
          CESSAELVAES.GEECRGIPGSVFKRTSPFLTHQVFNSYHSETNI.RYMKKLENKDISLVHSMIPLGSCT
Retrocopy CESSAELVAESIGEECRGIPGSVFKRTSPFLTHQVFNSYHSETNIFRYMKKLENKDISLVHSMIPLGSCT

Parental  MKLNSSSELAPITWKEFANIHPFVPLDQAQGYQQLFRELEKDLCELTGYDQVCFQPNSGAQGEYAGLATI
          MKLNSSSELAP.TWKEFANI.PFVPLDQAQGYQQLFRELEKDLCELTGYDQVCFQPNSGAQGEYAGLATI
Retrocopy MKLNSSSELAPMTWKEFANIYPFVPLDQAQGYQQLFRELEKDLCELTGYDQVCFQPNSGAQGEYAGLATI

Parental  RAYLNQKGEGHRTVCLIPKSAHGTNPASAHMAGMKIQPVEVDRYGNIDAVHLKAMVDKHKENLAAIMITY
          RAYLNQKGE.HRTVCLIPKSAHGTNPASAH.AGMKIQPVEVD..GNIDAVHLKAMVDKHKENLAAIMITY
Retrocopy RAYLNQKGERHRTVCLIPKSAHGTNPASAHIAGMKIQPVEVDKCGNIDAVHLKAMVDKHKENLAAIMITY

Parental  PSTNGVFEENISDVCDLIHQHGGQVYLDGANMNAQVGICRPGDFGSDVSHLNLHKTFCIPHGGGGPGMGP
          PSTNGVFEENISD.CDLIHQHGGQVYLDGANMNAQVGIC.PGDFGSDVSHLNLHKTFC.PHGGGGPGMGP
Retrocopy PSTNGVFEENISDMCDLIHQHGGQVYLDGANMNAQVGICHPGDFGSDVSHLNLHKTFCFPHGGGGPGMGP

Parental  IGVKKHLAPFLPNHPIISLKRNEDACPVGTVSAAPWGSSSILPISWAYIKMMGGK-GLKQATETAILNAN
          IGVKKHLAPFL.NHPIISLKRNEDACPVGTVS.AP.GSSSILPISWAYIKMMGGK.GLKQATETAILNAN
Retrocopy IGVKKHLAPFLANHPIISLKRNEDACPVGTVSEAPRGSSSILPISWAYIKMMGGK<GLKQATETAILNAN

Parental  YMAKRLEKHYRILFRGARGYVGHEFILDTRPFKKSANIEAVDVAKRLQDYGFHAPTMSWPVAGTLMVEPT
          YMAKRLEKHYRILFRGARGYVGHEFILDTRPFKKSANIEAVDVAKRLQDYGFHAPT..WPVAGTLMVEPT
Retrocopy YMAKRLEKHYRILFRGARGYVGHEFILDTRPFKKSANIEAVDVAKRLQDYGFHAPTVPWPVAGTLMVEPT

Parental  ESEDKAELDRFCDAMISIRQEIADIEEGRIDPRVNPLKMSPHSLTCVTSSCWDRPYSREVAAFPLPFVKP
          ESEDKAELD.FCDAMISIRQEIADIEEGRIDPRVNPLKMSPHSLTC.TSS.WDRPYSREVAAFPLPFVKP
Retrocopy ESEDKAELDSFCDAMISIRQEIADIEEGRIDPRVNPLKMSPHSLTCITSSHWDRPYSREVAAFPLPFVKP

Parental  ENKFWPTIARIDDIYGDQHLVCTCPPMEVYESPFSEQKRASS
          ENKFWP.IARIDDIYGDQHLVC.CPPMEVYESPFSEQKRASS
Retrocopy ENKFWPMIARIDDIYGDQHLVCNCPPMEVYESPFSEQKRASS

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	6.25 RPM
SRP007412_cerebellum	0.00 RPM	2.43 RPM
SRP007412_heart	0.06 RPM	0.03 RPM
SRP007412_kidney	0.30 RPM	32.22 RPM
SRP007412_liver	0.18 RPM	75.68 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2521 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2521 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2521 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2932
Pan troglodytes	retro_ptro_2060
Gorilla gorilla	retro_ggor_2034

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000178445	1 retrocopy	retro_hsap_2932,
Gorilla gorilla	ENSGGOG00000004507	1 retrocopy	retro_ggor_2034,
Macropus eugenii	ENSMEUG00000001734	1 retrocopy	retro_meug_2056,
Pongo abelii	ENSPPYG00000019225	1 retrocopy	retro_pabe_2521 ,
Pan troglodytes	ENSPTRG00000029347	1 retrocopy	retro_ptro_2060,