RetrogeneDB ID: retro_pvam_82

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_1260:141008..141555(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TIMP2
• Ensembl ID: ENSPVAG00000007452
• Aliases: None
• Description: TIMP metallopeptidase inhibitor 2 [Source:HGNC Symbol;Acc:11821]

Sequence

>retro_pvam_82
CAACAGGCATTTTGCAACACAGATGTAGCGATTAGGACCAAAGTGGTCAGTGAGGAATTGGACTCTGGGAACGACATCTA
CAGGAACCCCATCAAGAGGATTCAGATGAGATCAAGCAAATAAAGATGTTCGAAGGATCTGACAAGGACACAGAGTTTAT
CTACACGGCCCCCTCCTCTGCCACATGGGGGGTTTCACTGGACTTTGGAGGAAAAAAGAACATCTCATTGCAGGAAAGGC
CGAGGGGAACGGCAAGTTGTACATCACCCTCTGTGACTTCATCGTGCCTGAGGACACCCTGAGCACCACCCAGAAGAGCC
TGAACAGCACGTATCAGATGGGCTGCGAGTGTAAGATCACGTGCTACCCCAGGATCCCCTGCTACATCTCTCTGGGCCAG
TGCCTTTGGGTTGACTGGGTCATGCAAAAGAATAGCAACAGGCACCAGGCCAAGTTCTTTGCCTGTATCAAGAGAAGTGA
CCGGCTCCTGTGGTTGGTACCACAGGGCCCCGCCCCCAAGCACGACTTTCTTGCCATCAAGGGCCCG

Alignment

ORF - retro_pvam_82 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.84 %
• Parental protein coverage: 84.55 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  QQAFCNADVVIRAKVVSEKEVDSGNDIYGNPIKRIQY-EIKQIKMFKGPDKDIEFIYTAPSSAICGVSLD
          QQAFCN.DV.IR.KVVSE.E.DSGNDIY.NPIKRIQ..EIKQIKMF.G.DKD.EFIYTAPSSA..GVSLD
Retrocopy QQAFCNTDVAIRTKVVSE-ELDSGNDIYRNPIKRIQM<EIKQIKMFEGSDKDTEFIYTAPSSATWGVSLD

Parental  VGGKK-EYLIAGKAEGNGKMYITLCDFIVPWDTLSTTQKKSLNHRYQMGCECKITRCPMIPCYISSPDEC
          .GGKK.E.LIAGKAEGNGK.YITLCDFIVP.DTLSTTQ.KSLN..YQMGCECKIT..P.IPCYIS....C
Retrocopy FGGKK<EHLIAGKAEGNGKLYITLCDFIVPEDTLSTTQ-KSLNSTYQMGCECKITCYPRIPCYISL-GQC

Parental  LWMDWVTEKNINGHQAKFFACIKRSD-GSCAWYRGAAP-PKQEFLDIEDP
          LW.DWV..KN.N.HQAKFFACIKRSD.GSC.WY..A.P.PK..FL.I..P
Retrocopy LWVDWVMQKNSNRHQAKFFACIKRSD>GSCGWYHRAPP<PKHDFLAIKGP

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_82 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Pteropus vampyrus	ENSPVAG00000007452	1 retrocopy	retro_pvam_82 ,