RetrogeneDB ID: retro_pvam_931

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_17396:5488..6330(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SF3B4
• Ensembl ID: ENSPVAG00000014171
• Aliases: None
• Description: splicing factor 3b, subunit 4, 49kDa [Source:HGNC Symbol;Acc:10771]

Sequence

>retro_pvam_931
AATGCCAACTATGCCATTAAAATCACCAACATGATCAAACTCTGTGGGAAGCCAATCCAAGTGAATAAGGCATCAGCTCA
CAACAAAGCCTGGATGTGGGGGCCAACATTTTCATTGAGAACCTGGCCCCAGAGATTGATGAGAAGCTGCTTTATGATAC
TTTCAGTGCCTTTGAGGTCATCTTACAAACACCCTCAAGATTATTCAGGATCCTGACACAGGGAACTCCAAAAGTTATGC
CTTTCTTAATTTTGCTTTGTTTGATGTTTTGGATGCAATAATTAAGGCCATGAATGGGCAGTACCACTGTAACTGCCCTA
TCATTGTGCCCTGTGCCTTCAAGAAGGACTCTAAGAGTGAAACCATGGCTCAGCAGAGGAAGGACTTCTGGCAGCCCAGA
ACCCACTCTCTCAGGCTAACTGCTCTCATAAATTGTTGTCAGACACACCCCTTACACCCTCTTTTCCCAAACTTGTGGTA
TCATCATTGGGGTCTGGGCTTCCTCCACCAGGCATGACTCCTCCTGGTTCATTCCCACCCTTAGTACCACCACCTGCAGC
CCTTTCACCTGTGATATTCCCAGCGATGCCCTTACTGCCTATTCTTCCTGAGGCTGGAGAGCCTGGTCCCCCATCAGCTG
GAACCCCAGGAGCTTGACATCCTGGACACAAGACACTCACATCCTCACCCATTCCCACTAGGTGGGATGCTCCATCCAAG
AATGTCTCAAATGCAGTTGGCTCACATGGCCCTCATGTCTTAGGACACCCCATGCTGGACCTCCAGGAATGGGGGGCAGC
CACCACCCTGACTACCAACTGGGCACGCCCCCCGAAGGGCCC

Alignment

ORF - retro_pvam_931 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.14 %
• Parental protein coverage: 66.27 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 8

Retrocopy - Parental Gene Alignment:

Parental  DADYAIKIMNMIKLYGKPIRVNKASAHNK-NLDVGANIFIGNLDPEIDEKLLYDTFSAFGVILQTP-KIM
          .A.YAIKI.NMIKL.GKPI.VNKASAHNK..LDVGANIFI.NL.PEIDEKLLYDTFSAF.VILQTP....
Retrocopy NANYAIKITNMIKLCGKPIQVNKASAHNK<SLDVGANIFIENLAPEIDEKLLYDTFSAFEVILQTPSRLF

Parental  R-DPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKDSKGE-RHGSAAERLLAAQNPL
          R.DPDTGNSK.YAF.NFA.FD..DA.I.AMNGQY.CN.PI.V..AFKKDSK.E..HGSA.E.LLAAQNPL
Retrocopy R<DPDTGNSKSYAFLNFALFDVLDAIIKAMNGQYHCNCPIIVPCAFKKDSKSE<NHGSAEEGLLAAQNPL

Parental  SQADRPHQLFADAPPPPSAPNPVVSSLGSGLPPPGMPPPGSFPPPVPPPGALPPGIPPAMPPPPMPPGAG
          SQA...H.L..D.P..PS.P..VVSSLGSGLPPPGM.PPGSFPP.VPPP.AL.P.I.PAMP..P..P.AG
Retrocopy SQANCSHKLLSDTPLTPSFPKLVVSSLGSGLPPPGMTPPGSFPPLVPPPAALSPVIFPAMPLLPILPEAG

Parental  GHGPPSAGTPGAGHPGH-GHSHPHPFPPGGMPHPGMSQMQLAH-HGPHGLGH-PHAGPPG-SGGQPPPRP
          ..GPPSAGTPGA.HPGH..HSHPHPFP.GGM.HP.MSQMQLAH.HGPH.LGH.PHAGPPG..GGQPPP..
Retrocopy EPGPPSAGTPGA*HPGH>RHSHPHPFPLGGMLHPRMSQMQLAH<HGPHVLGH<PHAGPPG<NGGQPPP*L

Parental  PP-GMPHPGP
          P..G.P..GP
Retrocopy PT>GTPPEGP

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_931 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 15 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012495	2 retrocopies	retro_btau_1385, retro_btau_592,
Canis familiaris	ENSCAFG00000011617	3 retrocopies	retro_cfam_585, retro_cfam_711, retro_cfam_729,
Callithrix jacchus	ENSCJAG00000000793	3 retrocopies	retro_cjac_1297, retro_cjac_1909, retro_cjac_638,
Cavia porcellus	ENSCPOG00000008267	1 retrocopy	retro_cpor_234,
Echinops telfairi	ENSETEG00000008963	1 retrocopy	retro_etel_1310,
Homo sapiens	ENSG00000143368	1 retrocopy	retro_hsap_1356,
Gorilla gorilla	ENSGGOG00000004761	1 retrocopy	retro_ggor_1056,
Macaca mulatta	ENSMMUG00000007256	1 retrocopy	retro_mmul_2191,
Mustela putorius furo	ENSMPUG00000005563	2 retrocopies	retro_mputfur_1105, retro_mputfur_648,
Oryctolagus cuniculus	ENSOCUG00000004614	1 retrocopy	retro_ocun_1239,
Pongo abelii	ENSPPYG00000000912	1 retrocopy	retro_pabe_1124,
Pan troglodytes	ENSPTRG00000001243	1 retrocopy	retro_ptro_930,
Pteropus vampyrus	ENSPVAG00000014171	1 retrocopy	retro_pvam_931 ,
Rattus norvegicus	ENSRNOG00000021181	1 retrocopy	retro_rnor_2350,
Ictidomys tridecemlineatus	ENSSTOG00000000684	2 retrocopies	retro_itri_1153, retro_itri_487,