RetrogeneDB ID: retro_pabe_3055

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 7:38152088..38153243(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TTC4
• Ensembl ID: ENSPPYG00000001312
• Aliases: None
• Description: tetratricopeptide repeat protein 4 [Source:RefSeq peptide;Acc:NP_001127131]

Sequence

>retro_pabe_3055
ATGGAGTAACCTGAGCAGGACCCCACCTCAGACGATGCCATGGACTCGTTCCTGGAAAAGTTCCAGAGCCAGCCTTACCG
TGGCGGCTTTCATGAGGACCAGTGGGAAGAGGAATTTGAAAAGGTCCCCCTGTTTATGAAGAAAGCACCATCAGAAATTG
ATCCCAGGGAGAATCCTGACTTGGCTTGTCTCCAGTCAATTATTTTTGATGAGGAGCATTCTCTAGAACAGGCCAAGACC
TATAAAGATGAGGGCAATGATTATTTTAAAGAAAAAGACTACAAGAAAGCTGTAATTTCCTACGCTGAAGGATTAAAGAA
GAAATGTGCAAATCCTGATTTGAATGCTGTCCTTTATACCAACCAGGCAGCAGCACAATACTATCTGGGCAATTTTCGTT
CTGCTCTCAGTGATGTGATAGCTGCCAAAAAGTTAAAACCCTGCTACCTCAAAGCAATAATAAGAGGTGCCTTATGCCAT
CTGGAACTGAAACACTTTGCCAAGGCTGTGAACTGATGTGATGAAGGACTGCAGATAGATGCCAAAGAGAAGAAGCTTCT
GGAAATGAGGGCTAAAGTAGACAAGCTGAAGCTAATTGAACAGAGGGATGTGAGGAAAGCCAACTTGGAAGAAAAGGAGA
GGAATCAGAATGAGGTTTCACTCCAGGATATCAAGGCTAGGAACATCAGGCTCTCTGAAGCTGCCTGTGAGGATGAAGTT
TCAGCCTCAGAAAGTCTAGGTGAGCTTTTCCTGGATGGACTCAGCTCTGAGAACCCCCATGGAGCCAGACTGAGTCTAGA
TGACCAGGGCAGGCTGAGCTGGCCTGTGCTCTTTCTGTACCCAGAGTATGCCCAATCAGACTTCATCTCTGCTTTTCATG
AGGACTCCAGGTTTATTGATCATCTAATGGTGATGTCTGGTGAAACACCCTCTTGGGACCTAGAGCAAAAATATTGCCCT
GATAATTTGGAGGTCTATATTGAGGATGAGGACAGGGCAGAACTGTACTGGGTGCCTGCCAAGAGCACCTTGTTGCAGGA
TCTACAGCACCACAGGTACTTTGTAAAAGCCCTGACACCAGCATTTTTGGTCTACGTAGGATCCAAACTTTTTTGAAAGA
ATTATCTCTGGGGGAGAAAGGTGCACCAGATAAGA

Alignment

ORF - retro_pabe_3055 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.66 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEQPGQDPTSEDVMDSFLEKFQSQPYRGGFHEDQWEEEFEKVPLFMTRAPSEIDPRENPDLACLQSIIFD
          ME.P.QDPTS.D.MDSFLEKFQSQPYRGGFHEDQWEEEFEKVPLFM..APSEIDPRENPDLACLQSIIFD
Retrocopy ME*PEQDPTSDDAMDSFLEKFQSQPYRGGFHEDQWEEEFEKVPLFMKKAPSEIDPRENPDLACLQSIIFD

Parental  EERSPEEQAKTYKDEGNDYFKEKDYKKAVISYTEGLKKKCADPDLNAVLYTNRAAAQYYLGNFRSALNDV
          EE.S.E.QAKTYKDEGNDYFKEKDYKKAVISY.EGLKKKCA.PDLNAVLYTN.AAAQYYLGNFRSAL.DV
Retrocopy EEHSLE-QAKTYKDEGNDYFKEKDYKKAVISYAEGLKKKCANPDLNAVLYTNQAAAQYYLGNFRSALSDV

Parental  TAARKLKPFHLKAIIRGALCHLELKHFAEAVNWCDEGLQIDAKEKKLLEMRAKADKLKRIEQRDVRKANL
          .AA.KLKP..LKAIIRGALCHLELKHFA.AVN.CDEGLQIDAKEKKLLEMRAK.DKLK.IEQRDVRKANL
Retrocopy IAAKKLKPCYLKAIIRGALCHLELKHFAKAVN*CDEGLQIDAKEKKLLEMRAKVDKLKLIEQRDVRKANL

Parental  KEKKERNQNEALLQAIKARNIRLSEAACEDEDSASEGLGELFLDGLSTENPHGARLSLDDQGRLSWPVLF
          .EK.ERNQNE..LQ.IKARNIRLSEAACEDE.SASE.LGELFLDGLS.ENPHGARLSLDDQGRLSWPVLF
Retrocopy EEK-ERNQNEVSLQDIKARNIRLSEAACEDEVSASESLGELFLDGLSSENPHGARLSLDDQGRLSWPVLF

Parental  LYPEYAQSDFISAFHEDSRFIDHLMVMFGETPSWDLEQKYCPDNLEVYFEDEDRAELYRVPAKSTLLQVL
          LYPEYAQSDFISAFHEDSRFIDHLMVM.GETPSWDLEQKYCPDNLEVY.EDEDRAELY.VPAKSTLLQ.L
Retrocopy LYPEYAQSDFISAFHEDSRFIDHLMVMSGETPSWDLEQKYCPDNLEVYIEDEDRAELYWVPAKSTLLQDL

Parental  QHQRYFVKALTPAFLVCVGSSPFCKNYLRGRKVYQIR
          QH.RYFVKALTPAFLV.VGS..F.KNYL.GRKV.QIR
Retrocopy QHHRYFVKALTPAFLVYVGSKLF*KNYLWGRKVHQIR

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	11.39 RPM
SRP007412_cerebellum	0.00 RPM	14.11 RPM
SRP007412_heart	0.00 RPM	7.16 RPM
SRP007412_kidney	0.03 RPM	16.57 RPM
SRP007412_liver	0.03 RPM	15.73 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3055 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3055 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3055 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000243725	1 retrocopy	retro_hsap_3843,
Pongo abelii	ENSPPYG00000001312	1 retrocopy	retro_pabe_3055 ,
Pan troglodytes	ENSPTRG00000041368	1 retrocopy	retro_ptro_2620,