RetrogeneDB ID: retro_pvam_287

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_2358:210206..210924(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL7
• Ensembl ID: ENSPVAG00000009292
• Aliases: None
• Description: ribosomal protein L7 [Source:HGNC Symbol;Acc:10363]

Sequence

>retro_pvam_287
AAAAAAAGCCAAATGCCAGAAACCCTTAAGAAAAAGCAAAGGAATTTCACAGAACTGAAGATCAAGCACCTGAGAAAGAA
GTTTGCCTAAAAGATGCTTCTAAAGGCAAGGAGGAAGCTTATCTATGACAGAGCTAAGCACTATCACAAAGAATATAGAC
AGATGTACAGAACTAAGATTCAGATGGCTAGGATGACAAGAAAAGCTGGCAACTTCTATGTACCTGCAGAACCCAAATTG
GCATTTGTCGTCAGGATCAGAGGCATCAACAGTGTGAGCCCCAAGATCTGAAAGGTGCTACAGCTTCTGCGCCTTTGCTA
GATTTTTAATGGCACCTTTGTTAAGCTCAACAAGGCTTCCATTAACATACTGAGGATCACAGAGCCATACATCGCCTGGA
GGTACCCAAACCTGAAGTCAGTTAGGGAATTGATCTACAAGTGTCATTATGGCAAAATCAATAAAAAGTGAATTGCCCTG
ACAGATAACACATTGATTGCTCATTCTCTTGGTAAATATGGCATCATCTGCATGGAGGATCTGATTCATGAGATCTATAC
TATTGGAAAATGGTTCAAGAAGCAAACAACTTCCTATGGCCCTTCAAGTTGTCTTCTCCACAAGGTTTGGAATGAAGCAA
AAGATCACCCATTTTGTAGAAGGTAGAGATGCTGGCAACAGGGAAGACCAGATCAACAGGCTTATTAGAAGGATGAAC

Alignment

ORF - retro_pvam_287 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.0 %
• Parental protein coverage: 92.61 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KVPAVPETLKKKRRNFAELKIKRLRKKFAQKMLRKARR-LIYEKAKHYHKEYRQMYRTEIRMARMARKAG
          K....PETLKKK.RNF.ELKIK.LRKKFA.KML.KARR.LIY..AKHYHKEYRQMYRT.I.MARM.RKAG
Retrocopy KKSQMPETLKKKQRNFTELKIKHLRKKFA*KMLLKARRKLIYDRAKHYHKEYRQMYRTKIQMARMTRKAG

Parental  NFYVPAEPKLAFVIRIRGINGVSPKVRKVLQLLRLRQIFNGTFVKLNKASINMLRIVEPYIAWGYPNLKS
          NFYVPAEPKLAFV.RIRGIN.VSPK..KVLQLLRL..IFNGTFVKLNKASIN.LRI.EPYIAW.YPNLKS
Retrocopy NFYVPAEPKLAFVVRIRGINSVSPKI*KVLQLLRLC*IFNGTFVKLNKASINILRITEPYIAWRYPNLKS

Parental  VNELIYKRGYGKINKKRIALTDNTLIARSLGKYGIICMEDLIHEIYTVGKRFKEANNFLWPFK-LSSPRG
          V.ELIYK..YGKINKK.IALTDNTLIA.SLGKYGIICMEDLIHEIYT.GK.FK.......P.....S.R.
Retrocopy VRELIYKCHYGKINKK*IALTDNTLIAHSLGKYGIICMEDLIHEIYTIGKWFKKQTTSYGPSS>VFSTRF

Parental  GMKKKTTHFVEGGDAGNREDQINRLIRRMN
          GMK.K.THFVEG.DAGNREDQINRLIRRMN
Retrocopy GMKQKITHFVEGRDAGNREDQINRLIRRMN

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_287 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 8 parental genes, and 52 retrocopies.

Species	Parental gene accession	Retrocopies number
Latimeria chalumnae	ENSLACG00000003571	1 retrocopy	retro_lcha_63,
Loxodonta africana	ENSLAFG00000017110	10 retrocopies	retro_lafr_140, retro_lafr_169, retro_lafr_334, retro_lafr_462, retro_lafr_47, retro_lafr_524, retro_lafr_694, retro_lafr_707, retro_lafr_816, retro_lafr_909,
Macropus eugenii	ENSMEUG00000016319	9 retrocopies	retro_meug_1002, retro_meug_1449, retro_meug_1942, retro_meug_1947, retro_meug_60, retro_meug_760, retro_meug_84, retro_meug_968, retro_meug_99,
Monodelphis domestica	ENSMODG00000007136	4 retrocopies	retro_mdom_1341, retro_mdom_1998, retro_mdom_371, retro_mdom_66,
Oryctolagus cuniculus	ENSOCUG00000008407	12 retrocopies	retro_ocun_109, retro_ocun_1164, retro_ocun_1282, retro_ocun_1342, retro_ocun_1494, retro_ocun_1646, retro_ocun_1879, retro_ocun_456, retro_ocun_501, retro_ocun_718, retro_ocun_727, retro_ocun_785,
Pteropus vampyrus	ENSPVAG00000008696	3 retrocopies	retro_pvam_1179, retro_pvam_1482, retro_pvam_975,
Pteropus vampyrus	ENSPVAG00000009292	10 retrocopies	retro_pvam_105, retro_pvam_109, retro_pvam_1192, retro_pvam_1221, retro_pvam_151, retro_pvam_287 , retro_pvam_308, retro_pvam_68, retro_pvam_69, retro_pvam_995,
Sus scrofa	ENSSSCG00000006182	3 retrocopies	retro_sscr_1138, retro_sscr_209, retro_sscr_796,