RetrogeneDB ID: retro_pvam_172

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_1741:54834..55400(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LSM12
• Ensembl ID: ENSPVAG00000013706
• Aliases: None
• Description: LSM12 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:26407]

Sequence

>retro_pvam_172
GCTCCTCTGGGTGAATACTTCCATTTTGAGAGCCAGGCATTGTACAGGATATGCCAGGAGCAGTGGCTGCAGGATGAGTT
GGTAGCCTTCGACTACCAGTCCAAAATGCTGGCTTTAAAATGTCCCTCTTCCAGTAGAAAGCCCAACCATGCAGACATCT
TGCTCATAAACTGATAATATGTTTCAGAAGTGGAAATAATGACCAAACAGAAACCCCTTCTCCCCTAGCTTCACTCAATG
TTAGGAAGCTTGCCAGCAAAGCACCAGACAGAGAAGAAACTGAGCCAGGTCTATGCAGTCAGTACTGGTGTCTCCCTAGA
GGGCCAGCAGCATTTCCAGACCATTCACAAGACCATTAAATACTGTAAATGGCAAGAAAAAAACATCACAGTCATGGAAG
AAATTCTTACACTCTCATATCAAGTAGGAAACTGTAAAGTCAGAGGGGGCATCCACTGAGCCATATATGCAAAACAGTTA
AAAGACATTTTAAACATATGGAAAGCCAAAAGATACAGCAGCGTTCACAAGCCCAGCAACCACAGAAAGAGTCTGCCTTG
TCATCC

Alignment

ORF - retro_pvam_172 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.01 %
• Parental protein coverage: 98.97 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  APPGEYFSVGSQVSCRTCQEQRLQGEVVAFDYQSKMLALKCPSSSGKPNHADILLINLQYVSDVEIINDR
          AP.GEYF...SQ...R.CQEQ.LQ.E.VAFDYQSKMLALKCPSSS.KPNHADILLIN..YVS.VEI....
Retrocopy APLGEYFHFESQALYRICQEQWLQDELVAFDYQSKMLALKCPSSSRKPNHADILLIN**YVSEVEIMTKQ

Parental  TETPPPLASLNVSKLASKARTEKEEKLSQAYAISAGVSLEGQQLFQTIHKTIKDCKWQEKNIVVMEEVVI
          ....P.L.S.....L..K..TEK..KLSQ.YA.S.GVSLEGQQ.FQTIHKTIK.CKWQEKNI.VMEE...
Retrocopy KPLLP*LHSM-LGSLPAKHQTEK--KLSQVYAVSTGVSLEGQQHFQTIHKTIKYCKWQEKNITVMEE-IL

Parental  TPPYQVENCK-GKEGSALSHVRKIVEKHFRDVESQKILQRSQAQQPQKEAALSS
          T..YQV.NCK....G..LSH..K.V..HF...ESQKI.QRSQAQQPQKE.ALSS
Retrocopy TLSYQVGNCK<SQRGHPLSHICKTVKRHFKHMESQKIQQRSQAQQPQKESALSS

Legend:

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

Expression

RNA-Seq

Pteropus vampyrus was not studied using RNA-Seq expression data.

ChIP-Seq

Pteropus vampyrus was not studied using ChIP-Seq data.

EST

Pteropus vampyrus was not studied using EST data.

TSS

Pteropus vampyrus was not studied using FANTOM5 data.

Lab

retro_pvam_172 was not experimentally validated.

Homology

Retrocopy orthology:

Pteropus vampyrus 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 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001198	1 retrocopy	retro_chof_1429,
Dipodomys ordii	ENSDORG00000016381	1 retrocopy	retro_dord_596,
Erinaceus europaeus	ENSEEUG00000002419	1 retrocopy	retro_eeur_603,
Echinops telfairi	ENSETEG00000008374	1 retrocopy	retro_etel_21,
Macropus eugenii	ENSMEUG00000007501	1 retrocopy	retro_meug_1462,
Myotis lucifugus	ENSMLUG00000006391	1 retrocopy	retro_mluc_2205,
Macaca mulatta	ENSMMUG00000006804	1 retrocopy	retro_mmul_3,
Oryzias latipes	ENSORLG00000011310	1 retrocopy	retro_olat_12,
Pteropus vampyrus	ENSPVAG00000013706	1 retrocopy	retro_pvam_172 ,
Tupaia belangeri	ENSTBEG00000012523	2 retrocopies	retro_tbel_3062, retro_tbel_60,