RetrogeneDB ID: retro_ptro_2536

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 7:62159635..62160994(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000042295
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: GABPA
• Ensembl ID: ENSPTRG00000013810
• Aliases: None
• Description: None

Sequence

>retro_ptro_2536
ATGACTAAAAGAGAAGCAGAGGAGCTGATAGAAATTGAGATTGATGGAACAGAGAAAGCAGAGTGCACAGAAGAAAGCAT
TGTAAAACAAACCTACGCGCCAGCTGAATGTGTAAGCCAGGCCATAGACATCAATGAACCAATAGGCAATTTAAAGAAAC
TGCTAGAACCAAGACTACAGTGTTCTTTGGATGCTCATGAAATTTGTCTGCAAGATATCCACCTGGATCCAGAACGAAGT
TTATTTGACCAAGGAGTAAAAACAGATGGAACTGTACAGCTTAGTGTACAGGTAATTTCTTACCAAGGAATTGAACCAAA
GTTAAACATCCTTGAAATTGTTAAACCTGCGGACACTGTTGAGGTTGTTATTGATCCAGATGCCCACCATGCTGAATCAG
AAGCACATCTTGTTGAAGAAGCTCAAGTGATAACTCTTGATGGCACAAAACACATCACAACCATTTCAGATGAAACTTCA
GAACAAGTGACAAGATGGGCTGCTGCACTGGAAGGCTATAGGAAAGAACAAGAACGCCTTGGGATACCCTATGATCCCAT
ACAGTGGTCCACAGACCAAGTCCTGCATTGGGTGGTTTGGGTAATGAAGGAATTCAGCATGACCGATATAGACCTCACCA
CACTCAACATTTCGGGGAGAGAATTATGTAGTCTCAACCAAGAAGATTTTTTTCAGCGGGTTCCTCGGGGAGAAATTCTC
TGGAGTCATCTGGAACTTCTCCGAAAATACGTATTGGCAAGTCAAGAACAACAGATGAATGAAATAGTTACAATTGATCA
ACCTGTGCAAATTATTCCAGCATCAGTGCAATCTGCTACACCTACTACCATTAAAGTTATAAATAGTAGTGTGAAGGCAG
CCAAAGTACAAAGAGCGCCGAGGATTTCAGAAGATAGAAGCTCACCTGGGAACAGAACAGGAAACAATGGCCAAATCCAA
CTATGGCAGTTTTTGCTAGAACTTCTTACTGATAAGGACGCTTGAGACTGTATTTCTTGGGTTGGTGATGAAGGTGAATT
TAAGCTAAATCAGCCTGAACTGGTTGCACAAAAATGGGGACAGAGTAAAAATAAGCCTACGATGAACTATGAGAAACTCA
GTCGTGCATTCAGATATTATTATGATGGGGACATGATTTGTAAAGTTCAAGGCAAGAGATTTGTGCACAAGTTTGTCTGT
GACTTGAAGACTCTTACTGGATACAGTGCAGCGGAGTTGAACCGTTTGGTCACAGAATGTGAACAGAAGAAACTTGCAAA
GATGCAGCTCCATGGAATTGCCCAGCCAGTCACAGCAGTAGCTCTGGCTACTCCTTCTCTGCAAACGGAAAAGGATAAT

Alignment

ORF - retro_ptro_2536 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.8 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MTKREAEELIEIEIDGTEKAECTEESIVEQTYAPAECVSQAIDINEPIGNLKKLLEPRLQCSLDAHEICL
          MTKREAEELIEIEIDGTEKAECTEESIV.QTYAPAECVSQAIDINEPIGNLKKLLEPRLQCSLDAHEICL
Retrocopy MTKREAEELIEIEIDGTEKAECTEESIVKQTYAPAECVSQAIDINEPIGNLKKLLEPRLQCSLDAHEICL

Parental  QDIQLDPERSLFDQGVKTDGTVQLSVQVISYQGIEPKLNILEIVKPADTVEVVIDPDAHHAESEAHLVEE
          QDI.LDPERSLFDQGVKTDGTVQLSVQVISYQGIEPKLNILEIVKPADTVEVVIDPDAHHAESEAHLVEE
Retrocopy QDIHLDPERSLFDQGVKTDGTVQLSVQVISYQGIEPKLNILEIVKPADTVEVVIDPDAHHAESEAHLVEE

Parental  AQVITLDGTKHITTISDETSEQVTRWAAALEGYRKEQERLGIPYDPIQWSTDQVLHWVVWVMKEFSMTDI
          AQVITLDGTKHITTISDETSEQVTRWAAALEGYRKEQERLGIPYDPIQWSTDQVLHWVVWVMKEFSMTDI
Retrocopy AQVITLDGTKHITTISDETSEQVTRWAAALEGYRKEQERLGIPYDPIQWSTDQVLHWVVWVMKEFSMTDI

Parental  DLTTLNISGRELCSLNQEDFFQRVPRGEILWSHLELLRKYVLASQEQQMNEIVTIDQPVQIIPASVQSAT
          DLTTLNISGRELCSLNQEDFFQRVPRGEILWSHLELLRKYVLASQEQQMNEIVTIDQPVQIIPASVQSAT
Retrocopy DLTTLNISGRELCSLNQEDFFQRVPRGEILWSHLELLRKYVLASQEQQMNEIVTIDQPVQIIPASVQSAT

Parental  PTTIKVINSSAKAAKVQRAPRISGEDRSSPGNRTGNNGQIQLWQFLLELLTDKDARDCISWVGDEGEFKL
          PTTIKVINSS.KAAKVQRAPRIS.EDRSSPGNRTGNNGQIQLWQFLLELLTDKDA.DCISWVGDEGEFKL
Retrocopy PTTIKVINSSVKAAKVQRAPRIS-EDRSSPGNRTGNNGQIQLWQFLLELLTDKDA*DCISWVGDEGEFKL

Parental  NQPELVAQKWGQRKNKPTMNYEKLSRALRYYYDGDMICKVQGKRFVYKFVCDLKTLIGYSAAELNRLVTE
          NQPELVAQKWGQ.KNKPTMNYEKLSRA.RYYYDGDMICKVQGKRFV.KFVCDLKTL.GYSAAELNRLVTE
Retrocopy NQPELVAQKWGQSKNKPTMNYEKLSRAFRYYYDGDMICKVQGKRFVHKFVCDLKTLTGYSAAELNRLVTE

Parental  CEQKKLAKMQLHGIAQPVTAVALATASLQTEKDN
          CEQKKLAKMQLHGIAQPVTAVALAT.SLQTEKDN
Retrocopy CEQKKLAKMQLHGIAQPVTAVALATPSLQTEKDN

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	10.87 RPM
SRP007412_cerebellum	0.00 RPM	14.84 RPM
SRP007412_heart	0.00 RPM	16.09 RPM
SRP007412_kidney	0.00 RPM	17.34 RPM
SRP007412_liver	0.00 RPM	10.61 RPM
SRP007412_testis	0.21 RPM	35.51 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2536 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2536 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2536 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3737

---

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000013817	1 retrocopy	retro_cjac_2487,
Dasypus novemcinctus	ENSDNOG00000016059	1 retrocopy	retro_dnov_476,
Homo sapiens	ENSG00000154727	1 retrocopy	retro_hsap_3737,
Ochotona princeps	ENSOPRG00000009283	1 retrocopy	retro_opri_1174,
Pan troglodytes	ENSPTRG00000013810	1 retrocopy	retro_ptro_2536 ,
Tursiops truncatus	ENSTTRG00000004785	1 retrocopy	retro_ttru_154,