RetrogeneDB ID: retro_pvam_645

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_538:108259..108760(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MCTS1
• Ensembl ID: ENSPVAG00000013249
• Aliases: None
• Description: malignant T cell amplified sequence 1 [Source:HGNC Symbol;Acc:23357]

Sequence

>retro_pvam_645
AAATTTGATGAAAAAGAAAATGTGTCCAATTGCATCCAGGTGAAAACCTCAGTTATAAAGGGTCCTAAGAACTATTTGAT
AGAGCCATCTTTAGGTATTGAAACATGGTTTAATCAAATCATGCCTAAGAAAGATTCTGCCAAAATAGCATGATGCCACG
AACATATAGAAATCCTTACAGTAAGTGGAGAGTTACTGTTTTTTAGACAAAAAGAAGGACCTTTTTATCTAACCCTAAGA
TTACTTCACAAATATCCTTTTATCCTGCCACACCTGTAGGTTGAGAAAGGAGCCGTCAAATTTGTACTTAGCGGAGCAAA
TGTCATGTGTCCAGGTTTAACTTCTCCTGGAGCTAAACTTAACCCTGCTACAGTAAATGCGATTGTTGCTATCATGGCAG
AAGGAAAACAGTATGCTTTGTGTGTCAGAGTCATGAAGATCTCTGCAGGAGATATAGAGAAAGTCAACAAAGGAATTGGC
ATTGAAAATATCCATTATATT

Alignment

ORF - retro_pvam_645 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.25 %
• Parental protein coverage: 91.67 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RFDEKENVSNCIQLKTSVIKGIKNQLIEQFPGIEPWLNQIMPKKVPVKIVRCHEHIEILTVNG-LLFFRQ
          .FDEKENVSNCIQ.KTSVIKG.KN.LIE...GIE.W.NQIMPKK...KI..CHEHIEILTV.G.LLFFRQ
Retrocopy KFDEKENVSNCIQVKTSVIKGPKNYLIEPSLGIETWFNQIMPKKDSAKIA*CHEHIEILTVSGELLFFRQ

Parental  REGPFYPTLRLLHKYPFILPHQQVDKGAIKFLLSGANIICPGLTSPGAKLYPAVVDTIVAIMAEGKQHA-
          .EGPFY.TLRLLHKYPFILPH..V.KGA.KF.LSGAN..CPGLTSPGAKL.PA.V..IVAIMAEGKQ.A.
Retrocopy KEGPFYLTLRLLHKYPFILPHL*VEKGAVKFVLSGANVMCPGLTSPGAKLNPATVNAIVAIMAEGKQYAL

Parental  CVGIMKMSAEDIEKVNKRIGIEDIHYL
          CV..MK.SA.DIEKVNK.IGIE.IHY.
Retrocopy CVRVMKISAGDIEKVNKGIGIENIHYI

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_645 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 16 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000005502	1 retrocopy	retro_cpor_1411,
Erinaceus europaeus	ENSEEUG00000007258	1 retrocopy	retro_eeur_197,
Echinops telfairi	ENSETEG00000015462	1 retrocopy	retro_etel_19,
Homo sapiens	ENSG00000232119	1 retrocopy	retro_hsap_2422,
Gorilla gorilla	ENSGGOG00000009420	1 retrocopy	retro_ggor_1507,
Myotis lucifugus	ENSMLUG00000015101	1 retrocopy	retro_mluc_16,
Monodelphis domestica	ENSMODG00000010354	1 retrocopy	retro_mdom_203,
Mus musculus	ENSMUSG00000000355	3 retrocopies	retro_mmus_2504, retro_mmus_2505, retro_mmus_69,
Oryctolagus cuniculus	ENSOCUG00000014315	1 retrocopy	retro_ocun_212,
Pan troglodytes	ENSPTRG00000022241	1 retrocopy	retro_ptro_1396,
Pteropus vampyrus	ENSPVAG00000013249	3 retrocopies	retro_pvam_1323, retro_pvam_645 , retro_pvam_867,
Rattus norvegicus	ENSRNOG00000002563	2 retrocopies	retro_rnor_1841, retro_rnor_957,
Ictidomys tridecemlineatus	ENSSTOG00000011496	2 retrocopies	retro_itri_1136, retro_itri_1468,
Tupaia belangeri	ENSTBEG00000010666	2 retrocopies	retro_tbel_1485, retro_tbel_4265,
Tarsius syrichta	ENSTSYG00000001440	1 retrocopy	retro_tsyr_55,
Tursiops truncatus	ENSTTRG00000007208	1 retrocopy	retro_ttru_1587,