RetrogeneDB ID: retro_ptro_843

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 13:96771215..96771898(+)
• Located in intron of: ENSPTRG00000005979

Retrocopy information

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

Parental gene information

• Parental gene symbol: AMMECR1L
• Ensembl ID: ENSPTRG00000012437
• Aliases: None
• Description: None

Sequence

>retro_ptro_843
CCTCCACTGGAGTCCAAGTTGGCAGCAGGCTGTTGTGAGAGCAAGAAGCCCAAATTATCTGGAAGTGAAACACACAGTCA
CAAGAATGAGTCCACAGCCATCCCCAGCCCTAGGTCAGGACCTCTTCAAAACTGCCAGCATGTAGACAGCAGCAGCAGAT
AGGAGAGTGTGTTGGACTTAACTCTGGGACCTGGAAGTGCTCCCATCACACGAATGAATCCAGCATCAGGAGCACTGAGC
CCTCTCCCCCAGTCTAATGGAATGGCAGCTCCACAAAGAATCCGGAGGTGACTGCACAGATGTGCTGCTACTGCTTTACC
AAACTCCACTCTCAGCTCTATGGCTTTCCACAGCCACGACTTCCTAGATTCACCAATGACCCCTGTCTGCTCTTTGTGAC
ATGGAAGACAGGGAGGGACAAGTGGCTTCATGGCTGCATTGGGACCTTCTCAGCCATGAATCTTTATTCAGGTCTCAGGG
AATATGTTAGCCATTGCATTTAAGGACAGCTGATATCTCCTCCAATCTGAGAGGGGCTGCGTAAGCTTTTCTGCTCTGTC
TCCCTCCATACTAACTTTGAGGATGCTAGTGATTACCTGGACTGGGAGATAGGGGTCCATGGGATTTAAACTGAATTCAT
TAAGGAAAAAGGCATCAAACGTACAGCCTCATTTTCACCTGAG

Alignment

ORF - retro_ptro_843 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.61 %
• Parental protein coverage: 73.87 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PPLEPKLAAGCCGVKKPKLSGSGTHSHGNQSTTVPGSSSGPLQNHQHVDSSSGRENVSDLTLGPGNSPIT
          PPLE.KLAAGCC..KKPKLSGS.THSH.N.ST..P...SGPLQN.QHVDSSS..E.V.DLTLGPG..PIT
Retrocopy PPLESKLAAGCCESKKPKLSGSETHSHKNESTAIPSPRSGPLQNCQHVDSSSR*ESVLDLTLGPGSAPIT

Parental  RMNPASGALSPLPRPNGTA-NTTKNLVVTAEMCCYCFDVLYCHLYGFPQPRLPRFTNDPYPLFVTWKTGR
          RMNPASGALSPLP..NG.A...TKN..VTA.MCCYCF..L...LYGFPQPRLPRFTNDP..LFVTWKTGR
Retrocopy RMNPASGALSPLPQSNGMA<SSTKNPEVTAQMCCYCFTKLHSQLYGFPQPRLPRFTNDPCLLFVTWKTGR

Parental  DKRLRGCIGTFSAMNLHSGLREYTLTSALKDSRFPPLTREELPKLFCSVSLLTNFEDASDYLDWEVGVHG
          DK.L.GCIGTFSAMNL.SGLREY............P...E.L.KLFCSVSL.TNFEDASDYLDWE.GVHG
Retrocopy DKWLHGCIGTFSAMNLYSGLREY-VSHCI*GQLISPPI*EGLRKLFCSVSLHTNFEDASDYLDWEIGVHG

Parental  IRIEFINEKGVKRTATYLPE
          I..EFI.EKG.KRTA...PE
Retrocopy I*TEFIKEKGIKRTASFSPE

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	17.62 RPM
SRP007412_cerebellum	0.00 RPM	30.65 RPM
SRP007412_heart	0.00 RPM	13.26 RPM
SRP007412_kidney	0.00 RPM	28.71 RPM
SRP007412_liver	0.00 RPM	22.68 RPM
SRP007412_testis	0.11 RPM	53.11 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_843 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_843 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_843 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1227
Gorilla gorilla	retro_ggor_961
Macaca mulatta	retro_mmul_1302

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000009373	1 retrocopy	retro_chof_1566,
Callithrix jacchus	ENSCJAG00000010743	1 retrocopy	retro_cjac_383,
Equus caballus	ENSECAG00000023095	1 retrocopy	retro_ecab_1085,
Echinops telfairi	ENSETEG00000000510	1 retrocopy	retro_etel_9,
Homo sapiens	ENSG00000144233	1 retrocopy	retro_hsap_1227,
Gorilla gorilla	ENSGGOG00000014448	1 retrocopy	retro_ggor_961,
Myotis lucifugus	ENSMLUG00000006871	1 retrocopy	retro_mluc_684,
Macaca mulatta	ENSMMUG00000001987	1 retrocopy	retro_mmul_1302,
Mus musculus	ENSMUSG00000041915	2 retrocopies	retro_mmus_1330, retro_mmus_352,
Nomascus leucogenys	ENSNLEG00000015793	1 retrocopy	retro_nleu_700,
Pan troglodytes	ENSPTRG00000012437	1 retrocopy	retro_ptro_843 ,
Sarcophilus harrisii	ENSSHAG00000014762	1 retrocopy	retro_shar_86,