RetrogeneDB ID: retro_pvam_1160

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_33834:511..1056(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SUCLG1
• Ensembl ID: ENSPVAG00000003656
• Aliases: None
• Description: succinate-CoA ligase, alpha subunit [Source:HGNC Symbol;Acc:11449]

Sequence

>retro_pvam_1160
TTGCAACAGAATGGAAGTCAGCATTGTTCCTATACAGCTTCCCAGAAACATCTTTATGTTGATAAAAATACAAAGATTAT
TTGCAAGGGTTTCACTAGTAAACAGGGTACCTTTCATAGCCAACAGGCATTGGAATACGGTACCAGACTTGGAGGAACCA
CTCCAGGGAAAGGAAGCAAGATGTACCTGGGTTTACCTATCTTTAATACTATAAAGAAGCCCAAAGAATATATAGGAGCA
ACAGCTTCTGTCATTTATGTCGCTCCTCCTTTTGCTGCTGCTGCCATTTATGAATCTGTTGAGGCGGAAGTGCCTTTGAT
CCTGTGTATTACTGAAGGTATCCCACAAGAAGACATGTTTGGGTCAAGCACAGACTGTGTGCCAGAGAAAGACTGATGGG
GCCAAACTGTCCTGGAGTCATCAATCCTGGAGAATGCAAAATTGGCATCATGCCCAGCTGTATTCACAAGAAATAAAGAA
TTGGCATTGTGTCCAGGTCTGGTACCCTGACTGAAAGTAGTTCAACAAACACCAGTTGGGTTGGG

Alignment

ORF - retro_pvam_1160 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.42 %
• Parental protein coverage: 53.62 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LQQNGIRHCSYTASRKHLYVDKNTKIICQGFTGKQGTFHSQQALEYGTQLVGGTTPGKGGKTHLGLPVFN
          LQQNG..HCSYTAS.KHLYVDKNTKIIC.GFT.KQGTFHSQQALEYGT.L.GGTTPGKG.K..LGLP.FN
Retrocopy LQQNGSQHCSYTASQKHLYVDKNTKIICKGFTSKQGTFHSQQALEYGTRL-GGTTPGKGSKMYLGLPIFN

Parental  TVKEAKEQTGATASVIYVPPPFAAAAIDEAVEAEVPLVVCITEGIPQQDM-VRVKHRLLRQGKTRLIGPN
          T.K..KE..GATASVIYV.PPFAAAAI.E.VEAEVPL..CITEGIPQ.DM.V.VKHRL......RL.GPN
Retrocopy TIKKPKEYIGATASVIYVAPPFAAAAIYESVEAEVPLILCITEGIPQEDM<VWVKHRLC--ARERLMGPN

Parental  CPGVINPGECKIGIMPGHIHKKGRIGIVSRSGTLTYEAVHQTTQVG
          CPGVINPGECKIGIMP..IHKK.RIGIVSRSGTLT......T..VG
Retrocopy CPGVINPGECKIGIMPSCIHKK*RIGIVSRSGTLTESSSTNTSWVG

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_1160 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.

---

Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000003017	1 retrocopy	retro_cpor_1170,
Myotis lucifugus	ENSMLUG00000012370	1 retrocopy	retro_mluc_1231,
Procavia capensis	ENSPCAG00000013405	1 retrocopy	retro_pcap_356,
Pteropus vampyrus	ENSPVAG00000003656	2 retrocopies	retro_pvam_1160 , retro_pvam_670,
Drosophila melanogaster	FBgn0004888	1 retrocopy	retro_dmel_47,