RetrogeneDB ID: retro_pabe_2453

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 4:91305205..91305862(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL19
• Ensembl ID: ENSPPYG00000012255
• Aliases: None
• Description: 39S ribosomal protein L19, mitochondrial [Source:RefSeq peptide;Acc:NP_001127477]

Sequence

>retro_pabe_2453
CAGTTCTTGAGTCCCTAATTCATTCCTCCAAGAGGAAGAATAAATCCTCCGAAATTTCAAATAGGAAGAAAAGTTATGTT
AGAAAGGAGAAAAGTACTCCACATTCCAGACTTCTATGTTGGAAGTATTCTTTGTGTTACTACAGCTGACTCATATGCCG
GTGAAAAAATCAGCCAGTTTCTGGGGATTTGCATCTAGAGATCAGGAAAAGGACTTGGGGCTACTTTTATCCTTAGGAAT
GTTATTGAAGGACAAGGTGTTAAGATTTGCTTTGAACTTTATAATCCTCGAATCCAGGAGATTCAAGTGGTCAAATTAGA
GAAATGGCTGGATGATAGCTTGCTGTGGTTACGAGATGCCCTTCCTGAATATAGCACTGTTGATGTGAATATGAAGCCAG
TAGCACAACAGCCTAGCCAAGAAGTTCCTGTTAATAAGCTGAAAGTGAAAATGAAGCCTCAGCCCTGGTCCAAATGCTGG
GACTGTCCAAATTTTAATATTTAAGGAATAATATTTGATCCTTGTTTCACTGAAGAACAAATGAAAGCAGCTTAGAAGTA
GAGACATCTGTGGCTTGAATTTGATATTATGAGGGAATATGATGCTTCAAAAATTGAAGCTGCAATATGGGATGAAATTG
AAGCATCTAGAAAGTCC

Alignment

ORF - retro_pabe_2453 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.0 %
• Parental protein coverage: 75.0 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RFLSPEFIPPRGRTDPLKFQMERKDMLERRKVLHIPEFYVGHILRVTTADPYASGKISQFLGICIQRSGR
          .FLSP.FIPPRGR..P.KFQ..RK.MLERRKVLHIP.FYVG.IL.VTTAD.YA..KISQFLGICI.RSG.
Retrocopy QFLSP*FIPPRGRINPPKFQIGRKVMLERRKVLHIPDFYVGSILCVTTADSYAGEKISQFLGICI*RSGK

Parental  GLGATFILRNVIEGQGVEICFELYNPRVQEIQVVKLEKRLDDSLLYLRDALPEYSTFDVNMKPEVQEPNQ
          GLGATFILRNVIEGQGV.ICFELYNPR.QEIQVVKLEK.LDDSLL.LRDALPEYST.DVNMKP..Q.P.Q
Retrocopy GLGATFILRNVIEGQGVKICFELYNPRIQEIQVVKLEKWLDDSLLWLRDALPEYSTVDVNMKPVAQQPSQ

Parental  KVPVNELKVKMKPKPWSKRWERPNFNIKGIRFDLCLTEEQMKEAQKWSQPWLEFDMMREYDTSKIEAAIW
          .VPVN.LKVKMKP.PWSK.W..PNFNI.GI.FD.C.TEEQMK.A.K....WLEFD.MREYD.SKIEAAIW
Retrocopy EVPVNKLKVKMKPQPWSKCWDCPNFNI*GIIFDPCFTEEQMKAA*K*RHLWLEFDIMREYDASKIEAAIW

Parental  KEIEASKRS
          .EIEAS..S
Retrocopy DEIEASRKS

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	6.14 RPM
SRP007412_cerebellum	0.00 RPM	6.93 RPM
SRP007412_heart	0.00 RPM	7.16 RPM
SRP007412_kidney	0.00 RPM	23.24 RPM
SRP007412_liver	0.00 RPM	21.60 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2453 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2453 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2453 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2957
Pan troglodytes	retro_ptro_2002
Gorilla gorilla	retro_ggor_2048

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000002266	1 retrocopy	retro_eeur_485,
Homo sapiens	ENSG00000115364	1 retrocopy	retro_hsap_2957,
Gorilla gorilla	ENSGGOG00000027896	1 retrocopy	retro_ggor_2048,
Loxodonta africana	ENSLAFG00000000146	1 retrocopy	retro_lafr_472,
Myotis lucifugus	ENSMLUG00000012774	1 retrocopy	retro_mluc_1308,
Pongo abelii	ENSPPYG00000012255	1 retrocopy	retro_pabe_2453 ,
Pan troglodytes	ENSPTRG00000012108	1 retrocopy	retro_ptro_2002,
Ictidomys tridecemlineatus	ENSSTOG00000002873	1 retrocopy	retro_itri_549,
Tupaia belangeri	ENSTBEG00000016470	1 retrocopy	retro_tbel_326,