RetrogeneDB ID: retro_pvam_1236

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_46484:926..1867(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MAPRE2
• Ensembl ID: ENSPVAG00000012260
• Aliases: None
• Description: microtubule-associated protein, RP/EB family, member 2 [Source:HGNC Symbol;Acc:6891]

Sequence

>retro_pvam_1236
AATGGCAAGAACAAAATGACATCATCCAAGATAATAGAACTATCATTCTTTTCTGGAAGTACACTATGTGTGGAGAATGT
TCCTACAGTTGAGGAATGGCAGTCAATGTGTATTCTACCTCAATAGTCCAGAGCAGACATGACATCATTGCATGGGTTAA
GGGTGTAGTATCTTTAAACTACACAAAAGTGAACAGCTTTGTTCAGAAGCAGCCTATTGCCAGTTCATGAAATGCTCTTT
CCAGGATGCACTAGTTTGAAGAAGTAAAATTTTAAGCAATGTTGGAGCATAAGTATATTCACAATTTTAAACTTCTGCAA
GCATCATTTAAGCGAATAAATGTTGATAAGATAATTCCAGTGGAGAAGCTAGTGAAAGAGCATTTCCAAGACAACCTGCA
TGCTATTCAGTGGTTTAAGCAAATCTGTGATACTAAGTACTATGGAAATGCCTAGCTACAAAAAAATGATCCTGTAGAAG
CATGACAAGGGCAAGATGCAATTCTTCCCTTGACTCTGGTAAACAGATCTTCAGCCTACCAAAAAAGTCTCACCATATAA
ACTCCCCACAGCAGGTGTGGCTAAATCAAGTCTAGCATCTAAACCAGGATCCACACCTTCTTGTCCCTCATAAGTCAAAA
GGACTTCATCCAGCAGTTCAACACTTAAATATGATAAAGATTTGGAAACACAGATTATATAGCTTAATGAACAGGTACAT
TCATTGAAATTTGCCCTTGAAAGCGTGGAAAGGAAAGGGATTTCTATTTTGGAAAGGTGAGAGAGATTGAGCTACTCTGT
CAAGAACATGGGCAGGAAAATGATGACCTCATGCAGTAACTAATGAAAGTTCTCTGTGCTTTGGATGAGCACGATTGCCA
CTGAGAATAGCTAGAAGCAAAGGAACAAGTCCACAAACAGTAGCCTCAGCAGCAGGAAGAG

Alignment

ORF - retro_pvam_1236 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.23 %
• Parental protein coverage: 96.63 %
• Number of stop codons detected: 10
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  NGENN-NDIIQDNGTIIPFRKHTVRGERSYSWGMAVNVYSTSITQETMSRHDIIAWVNDIVSLNYTKV-E
          NG.N..NDIIQDN.TII.F.K.T..GE.SYS.GMAVNVYSTSI.Q...SRHDIIAWV...VSLNYTKV.E
Retrocopy NGKNK<NDIIQDNRTIILFWKYTMCGECSYS*GMAVNVYSTSIVQ---SRHDIIAWVKGVVSLNYTKV<E

Parental  QLCSGAAYCQFM-DMLFPGCISLKK-VKFQAKLEHEYIHNFKLLQASFKRMNVDKVIPVEKLVKGRFQDN
          QLCS.AAYCQFM..MLFPGC.SLKK.VKF.A.LEH.YIHNFKLLQASFKR.NVDK.IPVEKLVK..FQDN
Retrocopy QLCSEAAYCQFM<EMLFPGCTSLKK<VKF*AMLEHKYIHNFKLLQASFKRINVDKIIPVEKLVKEHFQDN

Parental  LDFIQWFKKFYDANYDG----KEYDPVEARQGQDAIPPP-DPGEQIFNLPKKSHHANSP-TAGAAKSSPA
          L..IQWFK...D..Y.G.......DPVEA.QGQDAI.P..D.G.QIF.LPKKSHH.NSP.TAG.AKSS.A
Retrocopy LHAIQWFKQICDTKYYGNA*LQKNDPVEA*QGQDAILPL<DSGKQIFSLPKKSHHINSP<TAGVAKSSLA

Parental  SKPGSTPSRPSSAKRASSSSSASKSDKDLETQVIQLNEQVHSLKLALEGVE-KERDFYFGKLREIELLCQ
          SKPGSTPS.PS..KR.SSSSS..K.DKDLETQ.I.LNEQVHSLK.ALE.VE.KERDFYFGK.REIELLCQ
Retrocopy SKPGSTPSCPS*VKRTSSSSSTLKYDKDLETQII*LNEQVHSLKFALESVE<KERDFYFGKVREIELLCQ

Parental  EHGQENDNLVQRLMEVLYASDEHEGHPEEPEAEEQVHEQQPQQQEE
          EHGQEND.L.Q.LM.VL.A.DEH..H.E..EA.EQVH.Q.PQQQEE
Retrocopy EHGQENDDLMQ*LMKVLCALDEHDCH*E*LEAKEQVHKQ*PQQQEE

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_1236 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000010586	1 retrocopy	retro_mdom_1760,
Pteropus vampyrus	ENSPVAG00000012260	1 retrocopy	retro_pvam_1236 ,
Pteropus vampyrus	ENSPVAG00000015887	1 retrocopy	retro_pvam_1035,
Drosophila melanogaster	FBgn0027066	1 retrocopy	retro_dmel_83,