RetrogeneDB ID: retro_ptro_3265

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: X:123617157..123617943(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000041636
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MRRF
• Ensembl ID: ENSPTRG00000021324
• Aliases: None
• Description: None

Sequence

>retro_ptro_3265
ATGGCCTTGGGATTAAAGTGCTCCCACATGGTCCACCCTGCCTTTCGCAATTATCTTGCAGCCTCTATCAGACCCGTTTC
AGAAGTTACACTGAAGACAGTGTATGAAAGACAACATGGCCATAGGCAATACGTGGCCTATTCAGCTGTACCAGTCCACC
ATTTTGCTACCAAGAAAGCCAAAGCCAAAGGGAAAGGAAAGTCCCAAACCAGAGTGAATATTAGTGCTGCCTTTGTTGAG
GATATAATCAACTTGGAAGAGGTGAATGAAGAAATGAAGTCTGTGATAGAAGCACACAAGGATAATTTCAATAAGACTCT
CAATATAAGGACCTCACCAGGATCCCTTGACAAGATTGCTGTGGTAACTGCTGATGGAAAACTTGCTTTAAACCAGATTA
GGCAGATCTCCGTGAAGTTGCCACAGCTGATTTTGGTGAATATGGCCAGCTTCCCAGAGTGTACAGTTGCAGCTATCAAG
GCTATAAGAGAAAGTGGAATGAATCTGAACCCAGAAGTGGAAGGGACACTAATTCGGGTACCCATTCCCCAAGTAATCAG
AGAGCACAGAGAAATGCTGGTGAAACTGGCCAAACAGAACACCAACAAGGCCAAATACTCTTTACTGAAGGTTTGTACCA
ACGCAATGAACAAGCTGAAGAAATCCAAGGATACAGTCTCGGAGGACACCATTAGGCTAACAGAGAAACAGATCAGCCAA
ATGGCCGATGACACAGTGGCAGAACTGTACAGGCATCTGGCAGTGAAGAACAAAGAACTCCTTGGA

Alignment

ORF - retro_ptro_3265 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.46 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MALGLKCFRMVHPTFRNYLTASIRPVSEVTLKTVHERPHGHRQYMAYSAVPVRHFATKKAKAKGKGQSQT
          MALGLKC..MVHP.FRNYL.ASIRPVSEVTLKTV.ER.HGHRQY.AYSAVPV.HFATKKAKAKGKG.SQT
Retrocopy MALGLKCSHMVHPAFRNYLAASIRPVSEVTLKTVYERQHGHRQYVAYSAVPVHHFATKKAKAKGKGKSQT

Parental  RVNINAALVEDIINLEEVNEEMKSVIEALKDNFNKTLNIRTSPGSLDKIAVVTADGKLALNQISQISMKS
          RVNI.AA.VEDIINLEEVNEEMKSVIEA.KDNFNKTLNIRTSPGSLDKIAVVTADGKLALNQI.QIS.K.
Retrocopy RVNISAAFVEDIINLEEVNEEMKSVIEAHKDNFNKTLNIRTSPGSLDKIAVVTADGKLALNQIRQISVKL

Parental  PQLILVNMASFPECTAAAIKAIRESGMNLNPEVEGTLIRVPIPQVTREHREMLVKLAKQNTNKAKDSLRK
          PQLILVNMASFPECT.AAIKAIRESGMNLNPEVEGTLIRVPIPQV.REHREMLVKLAKQNTNKAK.SL.K
Retrocopy PQLILVNMASFPECTVAAIKAIRESGMNLNPEVEGTLIRVPIPQVIREHREMLVKLAKQNTNKAKYSLLK

Parental  VRTNSMNKLKKSKYTVSEDTIRLIEKQISQMADDTVAELDRHLAVKTKELLG
          V.TN.MNKLKKSK.TVSEDTIRL.EKQISQMADDTVAEL.RHLAVK.KELLG
Retrocopy VCTNAMNKLKKSKDTVSEDTIRLTEKQISQMADDTVAELYRHLAVKNKELLG

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	8.94 RPM
SRP007412_cerebellum	0.00 RPM	9.43 RPM
SRP007412_heart	0.06 RPM	15.80 RPM
SRP007412_kidney	0.03 RPM	23.09 RPM
SRP007412_liver	0.03 RPM	10.57 RPM
SRP007412_testis	0.11 RPM	20.97 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3265 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3265 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3265 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4897
Gorilla gorilla	retro_ggor_98
Pongo abelii	retro_pabe_80

---

Parental genes homology:

Parental genes homology involve 10 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000007351	1 retrocopy	retro_cpor_877,
Homo sapiens	ENSG00000148187	1 retrocopy	retro_hsap_4897,
Gorilla gorilla	ENSGGOG00000023499	1 retrocopy	retro_ggor_98,
Mus musculus	ENSMUSG00000026887	1 retrocopy	retro_mmus_340,
Nomascus leucogenys	ENSNLEG00000017177	1 retrocopy	retro_nleu_1263,
Pongo abelii	ENSPPYG00000019570	1 retrocopy	retro_pabe_80,
Pan troglodytes	ENSPTRG00000021324	1 retrocopy	retro_ptro_3265 ,
Rattus norvegicus	ENSRNOG00000025997	2 retrocopies	retro_rnor_1477, retro_rnor_2654,
Sarcophilus harrisii	ENSSHAG00000012469	2 retrocopies	retro_shar_610, retro_shar_704,
Tupaia belangeri	ENSTBEG00000016569	1 retrocopy	retro_tbel_4411,