RetrogeneDB ID: retro_mmul_1159

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 15:77015047..77015788(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATP6V1D
• Ensembl ID: ENSMMUG00000021418
• Aliases: None
• Description: V-type proton ATPase subunit D [Source:RefSeq peptide;Acc:NP_001182644]

Sequence

>retro_mmul_1159
ATGTCGGGCAAAGACGGAATTGAAATCTTTCCCTCGCGAATGGCACAGACCATCATGAAGGCTTGTTTAAAGGGAGCACA
GACAGGTCGAAAAATCCTGAAAAAAAAATCTGACGCCTTAACTCTTTGATTTCGACAGATCCTAAAGAAGATAATAGAGA
CTAAAATGTTGATGGGCGAAGTGATGAGAGAAGCTGCCTTTTCACTAGCTGAAGCGAAGTTCACAGCAGGTGACTTCAGC
ACTACAGTTATCCAAAATGTAAATAAAGCCCAAGTGAAGATTCAAGAGAAGAAAGATAATGTAGCAGGTGTTACTTTGCC
AGTATTTGAACATTACCCTGAAGGAACTGACAGTTATGAACTGACTGGTTTAGCCAGAGGTGGGGAACAGTTGGCTAAAT
TAAAGAGGAATTATGCCAAAGCAGTGGAACTACTGGTGGAACTAGCTTCGCTGCAGACTTCTTTTGTTTCTTTGGATGAA
GCTATTACGATAACCAACAGGCATGTAAATGCCATTGAACATGTCATCATTCCCCGGATTGAACGTACTCTTGCTTATAT
CATCACAGAGCTGGATGAGAGAGAGTGAGAAGAGTGCTATAGGTTAAAGAAAATACAGGAGAAGAAAAAGATTCTAAAGG
AAAAATCTGAGAAGGACTTGGAACAAAGGAGAGCAGCTGGAGAGGTGTTGGAGCCTGCTAATCTTCCAGCTGAAGAGAAG
GATGAGGATCTTCTGTTTGAA

Alignment

ORF - retro_mmul_1159 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.12 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSGKDRIEIFPSRMAQTIMKARLKGAQTGRNLLKKKSDALTLRFRQILKKIIETKMLMGEVMREAAFSLA
          MSGKD.IEIFPSRMAQTIMKA.LKGAQTGR..L...SDALTL.FRQILKKIIETKMLMGEVMREAAFSLA
Retrocopy MSGKDGIEIFPSRMAQTIMKACLKGAQTGRKILXXXSDALTL*FRQILKKIIETKMLMGEVMREAAFSLA

Parental  EAKFTAGDFSTTVIQNVNKAQVKIRAKKDNVAGVTLPVFEHYHEGTDSYELTGLARGGEQLAKLKRNYAK
          EAKFTAGDFSTTVIQNVNKAQVKI..KKDNVAGVTLPVFEHY.EGTDSYELTGLARGGEQLAKLKRNYAK
Retrocopy EAKFTAGDFSTTVIQNVNKAQVKIQEKKDNVAGVTLPVFEHYPEGTDSYELTGLARGGEQLAKLKRNYAK

Parental  AVELLVELASLQTSFVTLDEAIKITNRRVNAIEHVIIPRIERTLAYIITELDEREREEFYRLKKIQEKKK
          AVELLVELASLQTSFV.LDEAI.ITNR.VNAIEHVIIPRIERTLAYIITELDERE.EE.YRLKKIQEKKK
Retrocopy AVELLVELASLQTSFVSLDEAITITNRHVNAIEHVIIPRIERTLAYIITELDERE*EECYRLKKIQEKKK

Parental  ILKEKSEKDLEQRRAAGEVLEPANLLAEEKDEDLLFE
          ILKEKSEKDLEQRRAAGEVLEPANL.AEEKDEDLLFE
Retrocopy ILKEKSEKDLEQRRAAGEVLEPANLPAEEKDEDLLFE

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	0.34 RPM	101.63 RPM
SRP007412_brain_prefrontal_cortex	0.24 RPM	81.87 RPM
SRP007412_cerebellum	0.00 RPM	68.26 RPM
SRP007412_heart	0.00 RPM	28.56 RPM
SRP007412_kidney	1.17 RPM	69.25 RPM
SRP007412_liver	0.04 RPM	12.03 RPM
SRP007412_testis	0.15 RPM	119.45 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1159 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1159 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1159 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 15 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008240	1 retrocopy	retro_amel_332,
Bos taurus	ENSBTAG00000016309	2 retrocopies	retro_btau_1757, retro_btau_408,
Canis familiaris	ENSCAFG00000016369	2 retrocopies	retro_cfam_1186, retro_cfam_999,
Choloepus hoffmanni	ENSCHOG00000003733	5 retrocopies	retro_chof_1229, retro_chof_2711, retro_chof_54, retro_chof_926, retro_chof_938,
Cavia porcellus	ENSCPOG00000009085	1 retrocopy	retro_cpor_36,
Felis catus	ENSFCAG00000011078	1 retrocopy	retro_fcat_632,
Myotis lucifugus	ENSMLUG00000006244	5 retrocopies	retro_mluc_2345, retro_mluc_442, retro_mluc_540, retro_mluc_666, retro_mluc_94,
Macaca mulatta	ENSMMUG00000021418	1 retrocopy	retro_mmul_1159 ,
Monodelphis domestica	ENSMODG00000009896	5 retrocopies	retro_mdom_1196, retro_mdom_1522, retro_mdom_1730, retro_mdom_390, retro_mdom_594,
Mustela putorius furo	ENSMPUG00000007002	2 retrocopies	retro_mputfur_1381, retro_mputfur_748,
Otolemur garnettii	ENSOGAG00000015052	1 retrocopy	retro_ogar_966,
Sus scrofa	ENSSSCG00000002288	1 retrocopy	retro_sscr_357,
Ictidomys tridecemlineatus	ENSSTOG00000027710	1 retrocopy	retro_itri_383,
Vicugna pacos	ENSVPAG00000005696	1 retrocopy	retro_vpac_232,
Drosophila melanogaster	FBgn0040377	1 retrocopy	retro_dmel_70,