RetrogeneDB ID: retro_ptro_2620

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 7:44618001..44619156(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TTC4
• Ensembl ID: ENSPTRG00000041368
• Aliases: None
• Description: tetratricopeptide repeat domain 4 [Source:HGNC Symbol;Acc:12394]

Sequence

>retro_ptro_2620
ATGGAGTAACCTGAGCAGGACCCCACCTCAGACGATGCCATGGACTCGTTCCTGGAAAAGTTCCAGAGCCAGCCTTACCG
TGGTGGCTTTCATGAGAATCAGTGGGAAGAGGAATTTGAAAAGGTCCCCCTGTTTATGAAGAAAGTGCCATCAGAAATTG
ATCCCAGGGAGAATCCTGACTTGGCTTTTCTCCAGTCAATTATTTTTGATGAGGAGCATTCTCCAGAACAGGCCAAGACC
TATAAAGATGAGGGCAATGATTATTTTAAAGAAAAAGACTACAAGAAAGCTGTAATTTCCTACACTGAAGGATTAAAGAA
GAAATGTGCAAATCCTGATTTGAATGCTGTCCATTATACCAACCGGGCAGCAGCACAATACTATCTGGGCAATTTTCATT
CTGCTCTCAGTGATGTGACAGCTGCCAAAAAGTTAAAACCGTGCTACCTCAAAGCAATAATAAGAGGTGCCTTATGCCAT
CTGGAACTGAAACACTTTGCCAAGGCTGTGAACTGATGTGATGAGGGACTGCAGATAGATGCCAAAGAGAAGAAGCTTCT
GGAAATGAGGGCTAAAGTAGACAAGCTGAAGCTAATTGAACAGAGGGATGTGAGGAAAGCCAACTTGAAAGAAAAGGAGA
GGAATCAGAATGAAGTTTTACTCCAGGATATCAAGGCTAGGAATATCAGGCTCTCTGAAGCTGCCTGTGAGGATGAAGTT
TCAGCCTCAGAAGGTCTAGGTGAGCTTTTCCTGGATGGACTCAGCTCTGAGAACCCCCATGGAGCCAGACTGAGTCTAGA
TGACCAGGGCAGACTGAGCTGGCCTGTGCTCTTTCTGTACCCAGCGTATGCCCAATCGGACTTCATCTCTGCTTTTCATG
AGGACTCCAGGTTTATTGATCATCTAATGGTGATGTTTGGTGAAACACCCTCTTGGGACCTAGAGCAAAAATATTGCCCT
GATAATTTGGAGGTCTACACTGAGGATGAGGACAGGGCAGAACTGTACTGGGTGCCTGCCAAGAGCCCCTTGCTGCAGGA
TCTACAGCACCACAGGCACTTTGTAAAAGCCCTGACACCAGCATTTTTGGTCTGTGTAGGATCCAAACTTTTTTGAAAGA
ATTATCTCTGGGGGAGAAAGGTGCACCAGATAAGA

Alignment

ORF - retro_ptro_2620 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.41 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEQPGQDPTSDDVMDSFLEKFQSHPYRGGFHEDHWEKEFEKVPLFMTRAPSEIDPRENPDLACLQSIIFD
          ME.P.QDPTSDD.MDSFLEKFQS.PYRGGFHE..WE.EFEKVPLFM...PSEIDPRENPDLA.LQSIIFD
Retrocopy ME*PEQDPTSDDAMDSFLEKFQSQPYRGGFHENQWEEEFEKVPLFMKKVPSEIDPRENPDLAFLQSIIFD

Parental  EERSPEEQAKTYKDEGNDYFKEKDYKKAVISYTEGLKKKCADPDLNAVLYTNRAAAQYYLGNFCSALNDV
          EE.SPE.QAKTYKDEGNDYFKEKDYKKAVISYTEGLKKKCA.PDLNAV.YTNRAAAQYYLGNF.SAL.DV
Retrocopy EEHSPE-QAKTYKDEGNDYFKEKDYKKAVISYTEGLKKKCANPDLNAVHYTNRAAAQYYLGNFHSALSDV

Parental  TAARKLKPCHLKAIIRGALCHLELKHFAEAVNWCDEGLQIDAKEKKLLEMRAKADKLKRIEQRDVRKANL
          TAA.KLKPC.LKAIIRGALCHLELKHFA.AVN.CDEGLQIDAKEKKLLEMRAK.DKLK.IEQRDVRKANL
Retrocopy TAAKKLKPCYLKAIIRGALCHLELKHFAKAVN*CDEGLQIDAKEKKLLEMRAKVDKLKLIEQRDVRKANL

Parental  KEKKERNQNEALLQAIKARNIRLSETACEDEDSASEGLGELFLDGLSTENPHGARLSLDDQGRLSWPVLF
          KEK.ERNQNE.LLQ.IKARNIRLSE.ACEDE.SASEGLGELFLDGLS.ENPHGARLSLDDQGRLSWPVLF
Retrocopy KEK-ERNQNEVLLQDIKARNIRLSEAACEDEVSASEGLGELFLDGLSSENPHGARLSLDDQGRLSWPVLF

Parental  LYPEYAQSDFISAFHEDSRFIDHLMVMFGETPSWDLEQKYCPDNLEVYFEDEDRAELYRVPAKSTLLQVL
          LYP.YAQSDFISAFHEDSRFIDHLMVMFGETPSWDLEQKYCPDNLEVY.EDEDRAELY.VPAKS.LLQ.L
Retrocopy LYPAYAQSDFISAFHEDSRFIDHLMVMFGETPSWDLEQKYCPDNLEVYTEDEDRAELYWVPAKSPLLQDL

Parental  QHQRYFVKALTPAFLVCVGSSPFCKNYLRGRKVYQIR
          QH.R.FVKALTPAFLVCVGS..F.KNYL.GRKV.QIR
Retrocopy QHHRHFVKALTPAFLVCVGSKLF*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	17.45 RPM
SRP007412_cerebellum	0.00 RPM	13.01 RPM
SRP007412_heart	0.00 RPM	8.66 RPM
SRP007412_kidney	0.00 RPM	13.21 RPM
SRP007412_liver	0.00 RPM	13.13 RPM
SRP007412_testis	0.00 RPM	18.44 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2620 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2620 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2620 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3843
Gorilla gorilla	retro_ggor_2588
Macaca mulatta	retro_mmul_1616

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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 ,