RetrogeneDB ID: retro_pvam_1122

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_3111:73524..74123(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TFG
• Ensembl ID: ENSPVAG00000017331
• Aliases: None
• Description: TRK-fused gene [Source:HGNC Symbol;Acc:11758]

Sequence

>retro_pvam_1122
CAAGATGAAATCAATAAAAATGTCATGTCAGCGTTTGGGTTAACAGCCAATCAGGTTTAGGGCCACCCAGTGCTCCTGCG
GAAGATGGATCTGGAAACACCTAGCAGCATTGCTTCCTCCTCCGCAGCTCATCCACCAGGAGTTCAGCCACAACAGCCGC
CATGTACCGGAGCTCAGACACAAGCAGGCCAGATATTCCGACAGTAACAGTACATGCTACAGGCTGGTTATAGTGCTCAG
CTGCCACAGACGCGGGCTCAGCCTACACAGTGGTATGGTATTCAGCATTCACCAGGCTCTAGTCAGCAGATTGGGATCCC
AGAAGCCTCAGCAGTTGCAGGGCTATGACCAGCAACCAACTTTCCAGTCACAGCTCCTGCCCTTTCTGGTCATCCTCAGC
AACTGCTGGCTCAACCCACACAGCAGTAGCACGCGAGCAATTACCCTCCATGCACTTATGATACCCAGACTCTCAGCCTC
CTGTTTATACTGTGGCTGTGCTCACACCTGGAATAGCTCCAAACCAACCCGGGCCTATCAACTATACCAGGTTTTAGTTC
ACCTCCTGGAAGTATCTCACTCCTGGAAGTACCACGCCC

Alignment

ORF - retro_pvam_1122 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.37 %
• Parental protein coverage: 51.12 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 8

Retrocopy - Parental Gene Alignment:

Parental  QDEINKNVMSAFGLTDDQV-SGPPSAPAEDRSG-TPDSIASSSSAAHPPGVQPQQPPYTGAQTQAGQSEG
          QDEINKNVMSAFGLT..QV..GPPSAPAED.SG.TP.SIASSS.AAHPPGVQPQQPP.TGAQTQA....G
Retrocopy QDEINKNVMSAFGLTANQV<LGPPSAPAEDGSG>TPSSIASSS-AAHPPGVQPQQPPCTGAQTQA----G

Parental  QIYQQ--YPQQAGYGAQQPQAPPQPPQQYGIQYSAGYSQQTG-PQQPQQFQGYGQQPTSQAP-APAFSGQ
          QI..Q..Y..QAGY.AQ.PQ...QP.Q.YGIQ.S.G.SQQ.G..Q.PQQ.QGY.QQPT.Q...APA.SG.
Retrocopy QIFRQ*QYMLQAGYSAQLPQTRAQPTQWYGIQHSPGSSQQIG>SQKPQQLQGYDQQPTFQSQ<APALSGH

Parental  PQQLPAQPPQQYQASNYPPHTYATQT-SQPTNYTVAPASQPGMAPSQPG-AYQ-PRPGFTSPPGST-MTP
          PQQL.AQP.QQ..ASNYPP.TY.TQT.SQP..YTVA....PG.AP.QPG.AYQ...PGF.SPPGS...TP
Retrocopy PQQLLAQPTQQ*HASNYPPCTYDTQT<SQPPVYTVAVLT-PGIAPNQPG<AYQ<TIPGFSSPPGSI<LTP

Parental  PPSGP
          ....P
Retrocopy GSTTP

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_1122 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 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013928	1 retrocopy	retro_chof_406,
Homo sapiens	ENSG00000114354	1 retrocopy	retro_hsap_3459,
Macaca mulatta	ENSMMUG00000002863	1 retrocopy	retro_mmul_1760,
Nomascus leucogenys	ENSNLEG00000002849	1 retrocopy	retro_nleu_2712,
Ochotona princeps	ENSOPRG00000000781	3 retrocopies	retro_opri_34, retro_opri_849, retro_opri_958,
Pongo abelii	ENSPPYG00000013597	1 retrocopy	retro_pabe_2860,
Pan troglodytes	ENSPTRG00000015165	1 retrocopy	retro_ptro_2345,
Pteropus vampyrus	ENSPVAG00000017331	1 retrocopy	retro_pvam_1122 ,
Ictidomys tridecemlineatus	ENSSTOG00000025779	1 retrocopy	retro_itri_457,