RetrogeneDB ID: retro_pabe_63

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2b:6084525..6085791(-)
• Located in intron of: ENSPPYG00000012756

Retrocopy information

• Ensembl ID: ENSPPYG00000012757
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPPYG00000003107
• Aliases: None
• Description: None

Sequence

>retro_pabe_63
ATGTCCAGCCAGGTGGTGGGCATTGAGCCTCTCTACATCAAGGCAGAGCCGGCCAGCCCCGACAGTCCAAAGGGTTCCTC
TGAGACGGAAACCGAGCCTCCTGTGGCCCTGGCCCCTGGTCCAGCTCCCACTCGCTGCCTCCCAGGCCACAAGGAAGAGG
AGGATGGGGAGGGGGCTGGGCCTGGCGAGCAGGGCGGTGGGAAGCTGGTGCTCAGCTCCCTGCCCAAGCGCCTCTGCCTG
GTCTGTGGGGACGTGGCCTCCGGCTACCACTACGGTGTGGCATCCTGTGAGGCCTGCAAAGCCTTCTTCAAGAGGACCAT
CCAGGGGAGCATCGAGTACAGCTGTCTGGCCTCCAATGAGTGTGAGATCACCAAGCGGAGACGCAAGGCCTGCCAGGCCT
GCCGCTTCACCAAGTGCCTGCGGGTGGGCATGCTCAAGGAGGGAATGCGCCTGGACCGCGTCCGGGGTGGGCGGCAGAAG
TACAAGCGGCAGCCGGAGGTGGACCCACTGCCCTTCCCGGGCCCCTTCCCTGCTGGGCCCCTGGCAGTCGCTGGAGGTCC
CCGGAAGACAGCCCCAGTGAATGCACTGGTGTCTCATCTGCTGGTGGTTGAGCCTGAGAAGCTCTATGCCATGCCTGACC
CTGCAGGCCCTGATGGGCACCTCCCAGCCGTGGCTACCCTCTGTGACCTCTTTGACCGAGAGATCGTGGTCACCATCAGC
TGGGCCAAGAGCATCCCAGGCTTCTCATCACTGTCGCTGTCTGACCAGATGTCAGTACTGCAGAGCGTGTGGATGGAGGT
GCTGGTGCTGGGTGTGGCCCAGCGCTCATTGCCACTGCAGGATGAGCTGGCCTTCGCTGAGGATTTAGTCCTGGATGAAG
AGGGGGCACGGGCAGCTGGCCTGGGGGAACTGGGGGCTGCCCTGCTGCAACTAGTGCAGCGGCTGCAGGCCCTGCGGCTG
GAGCGAGAGGAGTATGTTCTACTGAAGGCCCTGGCCCTTGCCAATTCAGACTCTGTGCACATCGAAGATGCCGAGGCTGT
GGAGCAGCTGCGAGAAGCTCTGCACGAGGCCCTGCTGGAGTACGAAGCCGGCCGGGCTGGCCCCGGAGGGGGTGCTGAGC
GGTGGCGGGCGGGCAGGCTGCTGCTCACGCTACCGCTCCTCCGCCAGACAGCGGGCAAAGTGCTGCCCCGTTTCTATGGG
GTGAAGCTGGAGGGCAAGGTGCCCATGCACAAGCTGTTCTTGGAGATGCTCGAGGCCATGATGGAC

Alignment

ORF - retro_pabe_63 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.11 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSSQVVGIEPLYIKAEPASPDSPKGSSETETEPPVALAPGPAPTRCLPGHKEEEDGEGAGPGEQGGGKLV
          MSSQVVGIEPLYIKAEPASPDSPKGSSETETEPPVALAPGPAPTRCLPGHKEEEDGEGAGPGEQGGGKLV
Retrocopy MSSQVVGIEPLYIKAEPASPDSPKGSSETETEPPVALAPGPAPTRCLPGHKEEEDGEGAGPGEQGGGKLV

Parental  LSSLPKRLCLVCGDVASGYHYGVASCEACKAFFKRTIQGSIEYSCPASNECEITKRRRKACQACRFTKCL
          LSSLPKRLCLVCGDVASGYHYGVASCEACKAFFKRTIQGSIEYSC.ASNECEITKRRRKACQACRFTKCL
Retrocopy LSSLPKRLCLVCGDVASGYHYGVASCEACKAFFKRTIQGSIEYSCLASNECEITKRRRKACQACRFTKCL

Parental  RVGMLKEGVRLDRVRGGRQKYKRRPEVDPLPFPGPFPAGPLAVAGGPRKTAAPVNALVSHLLVVEPEKLY
          RVGMLKEG.RLDRVRGGRQKYKR.PEVDPLPFPGPFPAGPLAVAGGPRKT.APVNALVSHLLVVEPEKLY
Retrocopy RVGMLKEGMRLDRVRGGRQKYKRQPEVDPLPFPGPFPAGPLAVAGGPRKT-APVNALVSHLLVVEPEKLY

Parental  AMPDPAGPDGHLPAVATLCDLFDREIVVTISWAKSIPGFSSLSLSDQMSVLQSVWMEVLVLGVAQRSLPL
          AMPDPAGPDGHLPAVATLCDLFDREIVVTISWAKSIPGFSSLSLSDQMSVLQSVWMEVLVLGVAQRSLPL
Retrocopy AMPDPAGPDGHLPAVATLCDLFDREIVVTISWAKSIPGFSSLSLSDQMSVLQSVWMEVLVLGVAQRSLPL

Parental  QDELAFAEDLVLDEEGARAAGLGELGAALLQLVRRLQALRLEREEYVLLKALALANSDSVHIEDAEAVEQ
          QDELAFAEDLVLDEEGARAAGLGELGAALLQLV.RLQALRLEREEYVLLKALALANSDSVHIEDAEAVEQ
Retrocopy QDELAFAEDLVLDEEGARAAGLGELGAALLQLVQRLQALRLEREEYVLLKALALANSDSVHIEDAEAVEQ

Parental  LREALHEALLEYEAGRAGPGGGAERRRAGRLLLTLPLLRQTAGKVLAHFYGVKLEGKVPMHKLFLEMLEA
          LREALHEALLEYEAGRAGPGGGAER.RAGRLLLTLPLLRQTAGKVL..FYGVKLEGKVPMHKLFLEMLEA
Retrocopy LREALHEALLEYEAGRAGPGGGAERWRAGRLLLTLPLLRQTAGKVLPRFYGVKLEGKVPMHKLFLEMLEA

Parental  MMD
          MMD
Retrocopy MMD

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	0.61 RPM	2.99 RPM
SRP007412_cerebellum	0.61 RPM	2.31 RPM
SRP007412_heart	2.02 RPM	9.03 RPM
SRP007412_kidney	1.76 RPM	11.37 RPM
SRP007412_liver	1.22 RPM	4.74 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_63 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_63 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_63 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018030	3 retrocopies	retro_cjac_3845, retro_cjac_3982, retro_cjac_4023,
Echinops telfairi	ENSETEG00000000262	1 retrocopy	retro_etel_733,
Homo sapiens	ENSG00000173153	2 retrocopies	retro_hsap_1171, retro_hsap_1237,
Gorilla gorilla	ENSGGOG00000001333	1 retrocopy	retro_ggor_970,
Macaca mulatta	ENSMMUG00000017803	1 retrocopy	retro_mmul_1275,
Nomascus leucogenys	ENSNLEG00000004971	2 retrocopies	retro_nleu_2855, retro_nleu_2856,
Pongo abelii	ENSPPYG00000003107	1 retrocopy	retro_pabe_63 ,
Pan troglodytes	ENSPTRG00000003833	1 retrocopy	retro_ptro_851,