RetrogeneDB ID: retro_mmul_631

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 10:36819456..36820399(-)
• Located in intron of: ENSMMUG00000022283

Retrocopy information

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

Parental gene information

• Parental gene symbol: SF3A3
• Ensembl ID: ENSMMUG00000023199
• Aliases: None
• Description: None

Sequence

>retro_mmul_631
ATGGAGACAATACTGGTGCAGCAGCAGCGCTATCATGAGAAGGAAAGGCTCATGGACGTCATGGCCAAAGAGATGCTGAC
TAAGAAGTCCACGCTCCGGGACCAGATCAATTCTGATCACCGCACTCAGGTCATACAAGACAGGTATATGGAGGTCAGTG
GGAACCCGAGGGATTTGTATGATGATAAAGATGGATTACGAAAGGAGGAGCTCAATGCCATTTCAGGACCCAATGAGTTT
GCTGAATTCTATAATAGACTCAAGCAAATAAAGGAATTCCACCAGAAGCCCCCAAATGAGATCTGTGTGCCAATGTCAGT
GGAATTTGAGGAGCTCCTGAAGACTTCGAGAAAATCCAAGTTAAGAGGCACAAAACTTGGTGGAGTGGAGTTCACAGATG
AAGAGGGATGTATGTGGTCGTTACCTCGATCTCCATGACTGTTACCTCAAGTACATTAACCTGAAGGCATCTGAGAAGAT
GGATTATATCACATACCCGTCCATCTTTGACCAATTATCTGACATTCCTAAAGAAAGGAAGAATGCAGAGTGTAAGACAT
ACCTAGAGATGCTGCTTGAGTACCTTCAGGATTACACAGATAGAGTGAAGCCTCTCCAAGACCAGAATGAAATTTTTGGG
AAGATTCAGGCTGAGTCTGAGAAGAAATGGGAGAATGGGACCTTTCCTGGATGGCCGAAAGAGACAAGCGGTGCTCTGAC
CCATGCTGGAGCCCATCTTGACCTCTCCGCATTCTCCTCCAGGGAGGAGTTGGCCTCTCTGGGTTTGGACAGATTGAAAT
CTGCTCTCTTAGCTTTAGGCTTGAAATGTGGCGGGACCCTAGAACAGCGAGTCCAGAGACTATTCAGCACCAAAGGAAAG
TCCCTGGAGTCACCTGATAACTCTTTGTCTGCCAAAAATCCCAAGTCAAAGAGCACCAAGCGA

Alignment

ORF - retro_mmul_631 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.95 %
• Parental protein coverage: 62.65 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  METILEQQRRYHEEKERLMDVMAKEMLTKKSTLRDQINSDHRTRAMQDRYMEVSGNLRDLYDDKDGLRKE
          METIL.QQ.RYHE.KERLMDVMAKEMLTKKSTLRDQINSDHRT...QDRYMEVSGN.RDLYDDKDGLRKE
Retrocopy METILVQQQRYHE-KERLMDVMAKEMLTKKSTLRDQINSDHRTQVIQDRYMEVSGNPRDLYDDKDGLRKE

Parental  ELNAISGPNEFAEFYNRLKQIKEFHRKHPNEICVPMSVEFEELLKA-RENPSEEAQNLVEFTDE---EGY
          ELNAISGPNEFAEFYNRLKQIKEFH.K.PNEICVPMSVEFEELLK..RENPS.EAQNLVE..........
Retrocopy ELNAISGPNEFAEFYNRLKQIKEFHQKPPNEICVPMSVEFEELLKT>RENPS*EAQNLVEWSSQMKRDVC

Parental  GRYLDLHDCYLKYINLKASEEILFKMTFSTPLSIQQAYFTFAKNKRRWESKIYLEMLLEYLQDYTDRVKP
          GRYLDLHDCYLKYINLKASE....KM...T..SI........K.....E.K.YLEMLLEYLQDYTDRVKP
Retrocopy GRYLDLHDCYLKYINLKASE----KMDYITYPSIFDQLSDIPKERKNAECKTYLEMLLEYLQDYTDRVKP

Parental  ITCDNEVFPAKYAMFLERMWTNLTFILNLKETSSALTHAGAHLDLSAFSSWEELASLGLDRLKSALLALG
          ....NE.F..K.....E..W.N.TF....KETS.ALTHAGAHLDLSAFSS.EELASLGLDRLKSALLALG
Retrocopy LQDQNEIF-GKIQAESEKKWENGTFPGWPKETSGALTHAGAHLDLSAFSSREELASLGLDRLKSALLALG

Parental  LKCGGTLEERAQRLFSTKGKSLESLDTSLFAKNPKSKGTKR
          LKCGGTLE.R.QRLFSTKGKSLES.D.SL.AKNPKSK.TKR
Retrocopy LKCGGTLEQRVQRLFSTKGKSLESPDNSLSAKNPKSKSTKR

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	2.13 RPM	36.53 RPM
SRP007412_brain_prefrontal_cortex	2.22 RPM	26.58 RPM
SRP007412_cerebellum	2.91 RPM	26.54 RPM
SRP007412_heart	1.00 RPM	18.31 RPM
SRP007412_kidney	1.88 RPM	30.52 RPM
SRP007412_liver	0.63 RPM	14.41 RPM
SRP007412_testis	6.75 RPM	128.80 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_631 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_631 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_631 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2441
Pan troglodytes	retro_ptro_1411

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001262	1 retrocopy	retro_amel_485,
Canis familiaris	ENSCAFG00000003222	1 retrocopy	retro_cfam_176,
Callithrix jacchus	ENSCJAG00000002176	1 retrocopy	retro_cjac_4109,
Cavia porcellus	ENSCPOG00000008660	1 retrocopy	retro_cpor_658,
Homo sapiens	ENSG00000183431	2 retrocopies	retro_hsap_2441, retro_hsap_937,
Macropus eugenii	ENSMEUG00000002534	3 retrocopies	retro_meug_1135, retro_meug_1346, retro_meug_642,
Macaca mulatta	ENSMMUG00000023199	1 retrocopy	retro_mmul_631 ,
Monodelphis domestica	ENSMODG00000017729	1 retrocopy	retro_mdom_269,
Nomascus leucogenys	ENSNLEG00000011720	1 retrocopy	retro_nleu_2775,
Pan troglodytes	ENSPTRG00000000559	2 retrocopies	retro_ptro_1411, retro_ptro_649,
Sorex araneus	ENSSARG00000014204	1 retrocopy	retro_sara_407,