RetrogeneDB ID: retro_ptro_2060

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 4:73388721..73391787(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GLDC
• Ensembl ID: ENSPTRG00000029347
• Aliases: None
• Description: glycine dehydrogenase (decarboxylating) [Source:HGNC Symbol;Acc:4313]

Sequence

>retro_ptro_2060
ATGCAGTCCTGTGCCAGGGCGTGGGGGCTGCGCCTGGGCCGCGGGGTCGGGGACGGCCGCCGCCTGGCTGGGGGATCGGG
GCTGTGCTGGGCGCCGCGGGGCCGGGACAGCAGCAGTGGCGGCGGGGACAGCGCCGCGGCTGGGGCCTCGCCCCTCCTGG
AGCGCCTTCTGCCCAGACACGACGACTTCGCTCGGAGGCACATCGGCCCTGGGGACAAAGACCAGAGAGAGATGCTGCAG
ATCTTGGGGCTGGCGAGCATTGATGAATTGATCGAGAAGACGGTCCCTACCAACATCCGTTTGAAAAGACCCTTGAAAAT
GGAAGACCCTGTTTGTGAAAATGAAATCCTTGCAACTCTGCATGCCATTTCAAGCAAAAACCAGATCTGGAGATCCTATA
TTGGCATGGGCTATTATAACTGCTCAGTGCCACAGACGATTTTGCGGAACTTACTGGAGAACTCAGGATGGATCACCCAG
TATACTCCATACCAGCCTGAGGTGTCTCAGGGGAGGCTGGAGAGTTTACTCAACTACCAGACCATGGTGTGTGACATCAC
AGGCCTGGGCATGGCCAATGCATCCCTGCTGGATGAGGGGACTGCAGCTGCAGAGGCGCTGCAGCTGTGCTACAGACACA
ACAAGAGGAGGAAATTTTTTGTTGACTCCCGTTGCCACCCACAGACAATAGCTGTTTTCCAGACTCGAGCCAAATATACT
GGAGTCCTCACTGAGCTGAAGTTACCCTATGAAATGGACTTCAGTGGAAAAGATGTCAGCGGAGTGTTGTTCCAGTACCC
AGACACGGAGGGGAAGGTGGAAGACTTTACGGGACTCGTGGAGAGAGCTCATCAGAGTGGGAGCCTGGCCTGCTGTGTGT
GCTACTGACCTTTTAGCTTTGTGCATCTTGAGGCCACCGGGAGAATTTGGGGGTAGACATCTCCTTGGGCAGCTCCCAGA
GATTTGGAGTGCCTCTGGGCTATGGGGGACCCCACGCAGCATTTTTTGCCGTCCGAGAAAGCTTGGTGAGAATGATGCCT
GGAAGAATGGTGGGGGCAACAAGAGACGCCACTGGGAAAGAAGTGTATTGTCTTGCTCTTCAAACCAGGGAGCAACACAT
TCAGAGAGACAAGGCTACCAGCAACATCTGTACAGCTCAGGCCCTCTTGGCGAATATGGCAGCCATGTTTGCAATCTACC
ATTGTTCCCATGGGCTGGAGCATATTGCTAGGAGGGTACATAATGCCACTTTGATTTTGTCAGAAGGTCTCAAGCGAGCA
GGGCATCAACTCCAGCATGACCTGTTCTTTGATACCTTGAAGATTCAGTGTGGCTGCTCAGTGAAGGAGGTCTTGGGCAG
GGCTGCTCAGCGGCAGATCAATTTTCGGCTTTTTGAGGATGGCACACTTGGTATTTCTCTTGATGAAACAGTCAATGAAA
AAGATCTGGACGATTTGTTGTGGATCTTTGTTTGTGAGTCATCTGCAGAACTGGTTGCTGAAAGCATGGGAGAGGAGTGC
AGAGGTATTCCAGGGTCTGTGTTCAAGAGGACCAGCCCGTTCCTCACCCATCAAGTGTTCAACAGCTACCACTCTGAAAC
AAATATTGTCCGGTATATGAAGAAACTGGAAAATAAAGACATTTCCCTTGTTCACAGCATGATTCCACTGGGATCCTACA
CCATGAAACTGAACAGTTCGTCTGAACTCGCACCTATCACATGGAAAGAATTTGCAAACATCCACCCCTTTGTGCCTCTG
GACCAAGCTCAAGGATATCAGCAGCTTTTCTGAGAACTGGAGAAGGATTTGTGTGAACTCACAGGTTATGACCAGGTCTG
TTTCCAGCCAAACAGCGGAGCCCAGGAAGAATATGCTGGACTGGCCACTATCCGAGCCTACTTAAACCAGAAAGGAGAGG
GGCACAGAACGGTTTGCCTCATTCTGAAATCAACACATGGGACCAACCCAACAAGTGCCCACATGGCAGGCATGAAGATT
CAGCCTGTGGAGGTGGATAAATGTGGGAATATCAATGCAGTTCACCTCAAGGCCATGGTGGATAAGCACAAGGAGAACCT
AGCAGCCATCATGATTACATACCCATCCACCAATGGGGTGTTTGAAGAGAACATCAGTGACGTGTGTGACCTCATCCATC
AACATGGAGGATAGGTCTACCTAGACAGGGCAAATATGAACGCTCAGGTGGGAATCTGTCGCCCTGGAGACTTTGGGTCT
GATGTCTCGCACCTAAATCTTCACAAGACCTTCTGCATTCCCCACAGAGGAGGTGGTCCTGGCATGGGGCCCATTGGAGT
AAGAAATACCTTGCCCCGTTTTTGTCCAATTATCCCATCATTTCACTAAAATGGAATGAGGATGCCTGTCCTGTGGGAAC
CGTCAGTGCGGCCCCATGGGGCTCCAGTTCCATCTTGCCCATTTCCTGGGCTTATATCAAGATGATGGGAGGCAAGGGCC
TTAAACAAGCCACGGAAACTGCGATATTAAATGCCAATTACATGGCCAAGCGATTAGAAAAACACTACAGAATTCTTTTC
AGGGGTGCAAGAGGTTATGTGGGTCATGAATTTATTTTGGACACGAGAGCCTTCAAAAAGTCTGCAAATATTGAGGCAGT
GGATGTGGCCAAGAGACTCCAGGATTATGGATTTCACGCCCCTATCATGCCCTGGCCTGTGGCAGGGACCCTCATGGTTG
AGCCCACTGAGTCGGAGGACAAGGCAGAGCTGGACAGATTCTGTGATGCCATGATCAGCATTCGGCAGGAAATTGCTGAC
ATTGAGGAGGGCCGCATCGACCCCAGGGTCAATCTGCTGAAGATGTCTCCGCACTCCCTGACCTGCGTTATATCTTCCCA
CTGGGACCGGCCTTATATTCCAGAGAGGTGGCAGCATTCCCACTCCCCTTCGTGAAACCAGAGAACAAATTCTGGCCAAT
GATTGCCCGGATTGATGACATATATGGAGATCAGCACCTGGTTTGTACCTGCCCACCCATGGAAGTTTATGAGTCGCCAT
TTTCTGAACAAAAGAGGGCCTCTTCT

Alignment

ORF - retro_ptro_2060 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.83 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MQSCARAWGLRLGRGVGGGRRLAGGSGPCWAPRGRDSSSGGGDSAAAGASRLLERLLPRHDDFARRHIGP
          MQSCARAWGLRLGRGVG.GRRLAGGSG.CWAPRGRDSSSGGGDSAAAGAS.LLERLLPRHDDFARRHIGP
Retrocopy MQSCARAWGLRLGRGVGDGRRLAGGSGLCWAPRGRDSSSGGGDSAAAGASPLLERLLPRHDDFARRHIGP

Parental  GDKDQREMLQTLGLASIDELIEKTVPANIRLKRPLKMEDPVCENEILATLHAISSKNQIWRSYIGMGYYN
          GDKDQREMLQ.LGLASIDELIEKTVP.NIRLKRPLKMEDPVCENEILATLHAISSKNQIWRSYIGMGYYN
Retrocopy GDKDQREMLQILGLASIDELIEKTVPTNIRLKRPLKMEDPVCENEILATLHAISSKNQIWRSYIGMGYYN

Parental  CSVPQTILRNLLENSGWITQYTPYQPEVSQGRLESLLNYQTMVCDITGLDMANASLLDEGTAAAEALQLC
          CSVPQTILRNLLENSGWITQYTPYQPEVSQGRLESLLNYQTMVCDITGL.MANASLLDEGTAAAEALQLC
Retrocopy CSVPQTILRNLLENSGWITQYTPYQPEVSQGRLESLLNYQTMVCDITGLGMANASLLDEGTAAAEALQLC

Parental  YRHNKRRKFFVDPRCHPQTIAVVQTRAKYTGVLTELKLPCEMDFSGKDVSGVLFQYPDTEGKVEDFTELV
          YRHNKRRKFFVD.RCHPQTIAV.QTRAKYTGVLTELKLP.EMDFSGKDVSGVLFQYPDTEGKVEDFT.LV
Retrocopy YRHNKRRKFFVDSRCHPQTIAVFQTRAKYTGVLTELKLPYEMDFSGKDVSGVLFQYPDTEGKVEDFTGLV

Parental  ERAHQSGSLA-C-CATDLLALCILRPPGEFG-VDIALGSSQRFGVPLGYGGPHAAFFAVRESLVRMMPGR
          ERAHQSGSLA.C.CATDLLALCILRPPGEFG.VDI.LGSSQRFGVPLGYGGPHAAFFAVRESLVRMMPGR
Retrocopy ERAHQSGSLACC>CATDLLALCILRPPGEFG>VDISLGSSQRFGVPLGYGGPHAAFFAVRESLVRMMPGR

Parental  MVGVTRDATGKEVYRLTLQTREQHIRRDKATSNICTAQALLANMAAMFAIYHGSHGLEHIARRVHNATLI
          MVG.TRDATGKEVY.L.LQTREQHI.RDKATSNICTAQALLANMAAMFAIYH.SHGLEHIARRVHNATLI
Retrocopy MVGATRDATGKEVYCLALQTREQHIQRDKATSNICTAQALLANMAAMFAIYHCSHGLEHIARRVHNATLI

Parental  LSEGLKRAGHQLQHDLFFDTLKIQCGCSVKEVLGRAAQRQINFRLFEDGTLGISLDETVNEKDLDDLLWI
          LSEGLKRAGHQLQHDLFFDTLKIQCGCSVKEVLGRAAQRQINFRLFEDGTLGISLDETVNEKDLDDLLWI
Retrocopy LSEGLKRAGHQLQHDLFFDTLKIQCGCSVKEVLGRAAQRQINFRLFEDGTLGISLDETVNEKDLDDLLWI

Parental  FGCESSAELVAESMGEECRGIPGSVFKRTSPFLTHQVFNSYHSETNIVRYMKKLENKDISLVHSMIPLGS
          F.CESSAELVAESMGEECRGIPGSVFKRTSPFLTHQVFNSYHSETNIVRYMKKLENKDISLVHSMIPLGS
Retrocopy FVCESSAELVAESMGEECRGIPGSVFKRTSPFLTHQVFNSYHSETNIVRYMKKLENKDISLVHSMIPLGS

Parental  CTMKLNSSSELAPITWKEFANIHPFVPLDQAQGYQQLFRELEKDLCELTGYDQVCFQPNSGAQGEYAGLA
          .TMKLNSSSELAPITWKEFANIHPFVPLDQAQGYQQLF.ELEKDLCELTGYDQVCFQPNSGAQ.EYAGLA
Retrocopy YTMKLNSSSELAPITWKEFANIHPFVPLDQAQGYQQLF*ELEKDLCELTGYDQVCFQPNSGAQEEYAGLA

Parental  TIRAYLNQKGEGHRTVCLIPKSAHGTNPASAHMAGMKIQPVEVDKYGNIDAVHLKAMVDKHKENLAAIMI
          TIRAYLNQKGEGHRTVCLI.KS.HGTNP.SAHMAGMKIQPVEVDK.GNI.AVHLKAMVDKHKENLAAIMI
Retrocopy TIRAYLNQKGEGHRTVCLILKSTHGTNPTSAHMAGMKIQPVEVDKCGNINAVHLKAMVDKHKENLAAIMI

Parental  TYPSTNGVFEENISDVCDLIHQHGGQVYLDGANMNAQVGICRPGDFGSDVSHLNLHKTFCIPHGGGGPGM
          TYPSTNGVFEENISDVCDLIHQHGG.VYLD.ANMNAQVGICRPGDFGSDVSHLNLHKTFCIPH.GGGPGM
Retrocopy TYPSTNGVFEENISDVCDLIHQHGG*VYLDRANMNAQVGICRPGDFGSDVSHLNLHKTFCIPHRGGGPGM

Parental  GPIGV-KKHLAPFLPNHPVISLKRNEDACPVGTVSAAPWGSSSILPISWAYIKMMGGKGLKQATETAILN
          GPIGV.KK.LAPFL.N.P.ISLK.NEDACPVGTVSAAPWGSSSILPISWAYIKMMGGKGLKQATETAILN
Retrocopy GPIGV<KKYLAPFLSNYPIISLKWNEDACPVGTVSAAPWGSSSILPISWAYIKMMGGKGLKQATETAILN

Parental  ANYMAKRLEKHYRILFRGARGYVGHEFILDTRPFKKSANIEAVDVAKRLQDYGFHAPTMSWPVAGTLMVE
          ANYMAKRLEKHYRILFRGARGYVGHEFILDTR.FKKSANIEAVDVAKRLQDYGFHAP.M.WPVAGTLMVE
Retrocopy ANYMAKRLEKHYRILFRGARGYVGHEFILDTRAFKKSANIEAVDVAKRLQDYGFHAPIMPWPVAGTLMVE

Parental  PTESEDKAELDRFCDAMISIRQEIADIEEGRVDPRVNPLKMSPHSLTCVTSSHWDRPYSRE-VAAFPLP-
          PTESEDKAELDRFCDAMISIRQEIADIEEGR.DPRVN.LKMSPHSLTCV.SSHWDRPY..E.....P.P.
Retrocopy PTESEDKAELDRFCDAMISIRQEIADIEEGRIDPRVNLLKMSPHSLTCVISSHWDRPYIPE>GGSIPTP>

Parental  FVKPENKFWPTIARIDDIYGDQHLVCTCPPMEVYESPFSEQKRASS
          FVKPENKFWP.IARIDDIYGDQHLVCTCPPMEVYESPFSEQKRASS
Retrocopy FVKPENKFWPMIARIDDIYGDQHLVCTCPPMEVYESPFSEQKRASS

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	0.07 RPM	10.81 RPM
SRP007412_cerebellum	0.04 RPM	15.24 RPM
SRP007412_heart	0.00 RPM	0.35 RPM
SRP007412_kidney	0.26 RPM	232.44 RPM
SRP007412_liver	0.10 RPM	47.24 RPM
SRP007412_testis	0.11 RPM	12.22 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2060 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2060 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2060 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2932
Gorilla gorilla	retro_ggor_2034
Pongo abelii	retro_pabe_2521

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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 ,