RetrogeneDB ID: retro_meug_1346

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: Scaffold375992:1108..1632(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SF3A3
• Ensembl ID: ENSMEUG00000002534
• Aliases: None
• Description: splicing factor 3a, subunit 3, 60kDa [Source:HGNC Symbol;Acc:10767]

Sequence

>retro_meug_1346
GTGCCAATGTCACTGGAATTTGAAGAGCTCCTAAAATCCAAAGCAGATCCTCTGAAAAGGCACAACCCTTGGTGGAGCCC
ACAGATGAGGAGGGATATGACCTTTACCTGAACCTTCATGACTGTTCCCTTAAGTATATTAACTTGAAAGTATCTGAGAA
ACTGGATGGTACCATGTACTCATCTATCCTTGCCCAGATATTTGATATGCTCAAGGAAAGGAAGAGTGCAGAGTATAAGA
GGTACCTGGAGATACTGCTAGAACACCTCCAGAACTTCAGGGACAGGGTAAATCCCCTACAAGACCAGAATGAGCTGTTG
GGGAAGATTCAGAATGAGTTTGAGAAGTGGAACGATGGTACCTTGCTAGGCTGGCCAGAAGGGACAAGCAGCTCACTGAC
CCACACTGGGACCCATCTTGACCTCGCTGCATTTTCCTGCTGGGAGAAGGTGGCCTCCTTGGGCCTGGACAGACTAAAAT
CTGCACTTTTGGCTTTAGGAGTGAAATATGTTGGGACAGTGGAA

Alignment

ORF - retro_meug_1346 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.32 %
• Parental protein coverage: 52.54 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VPMSVEFEELLKARENP-SEEAQNLVEFTDEEGYGRYLDLHDCYLKYINLKASEKLDYITYLSIFDQLFD
          VPMS.EFEELLK....P.SE.AQ.LVE.TDEEGY..YL.LHDC.LKYINLK.SEKLD...Y.SI..Q.FD
Retrocopy VPMSLEFEELLKSKADP<SEKAQPLVEPTDEEGYDLYLNLHDCSLKYINLKVSEKLDGTMYSSILAQIFD

Parental  IPKERKNAEYKRYLEMLLEYLQDYTDRVKPLQDQNELFGKIQNEFEKKWDNGTFPGWPKETSSALTHAGA
          ..KERK.AEYKRYLE.LLE.LQ...DRV.PLQDQNEL.GKIQNEFEK.W..GT..GWP..TSS.LTH.G.
Retrocopy MLKERKSAEYKRYLEILLEHLQNFRDRVNPLQDQNELLGKIQNEFEK-WNDGTLLGWPEGTSSSLTHTGT

Parental  HLDLSAFSSWEELASLGLDRLKSALLALGLKCGGTLE
          HLDL.AFS.WE..ASLGLDRLKSALLALG.K..GT.E
Retrocopy HLDLAAFSCWEKVASLGLDRLKSALLALGVKYVGTVE

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Macropus eugenii was not studied using RNA-Seq expression data.

ChIP-Seq

Macropus eugenii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_meug_1346 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_1346 was not experimentally validated.

Homology

Retrocopy orthology:

Macropus eugenii does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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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,