RetrogeneDB ID: retro_amel_559

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192501.1:1828495..1829424(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF4B
• Ensembl ID: ENSAMEG00000012023
• Aliases: None
• Description: eukaryotic translation initiation factor 4B [Source:HGNC Symbol;Acc:3285]

Sequence

>retro_amel_559
AGCAGAGACTATGATTGAGGCTACGACTCAGGATTAAACAGCAGCAGCAGTATATGTGTTAGTGGGTACAATAGGGATAA
TGACTACAGACGAAGTGGGACCACCCGGAAGACCAATATGATAGACATGATGTTCAGTTGAGAAGCTCTAAAGATGATTA
TTCTGGGGATGATTACAGATATGATAACAGAGGTCCCTCCCAAAGAACCAAACTGAATCTAAAACTTCAGAGTACTCCTA
AGGAAGATGATTCCTTGGCTGGCACCTCCCAGTCTAGTCAAGCAGCTTCTATGTTTGGAGCAGCAAGGCCTATTGACCCA
GCTATAAGAGAACAAGAAGTAGAAAAGCAGCTACAGAAGGAACAGGAGAAATCGAATCATCAGCGAGATGAACCCGAACT
GGAATGACAGTCTCAGAAGAGATATCCAAAGTGGCAAAGTGAAAAAACTCAGGAACAAGAATGGTCAAGGACAGGAAGTT
TCTCATCTCAAACTGGGACCTCAGCCGCATCAGAAGTCAGAGCAGGATGCGCAAAGGAGAGAACCTGAGAAATCTGGAAA
AAGAAGTACTCAGTACGGCAGAAGACTGTCACTCTCCAACTTCTAATCTTGCCAAACATAACCAGCTGCTAAAGGTAATT
ATGTCCCCTCCATTAAAAGTGGATGCTTGGGTGAAGTGAAATGGTAATTCTTATGCTTAATTTCAGAGCTCAAACAGAAC
AGCAATCTCCTACAAGGGATGCGGGGAAAGTAGCTCCAGCTCAAACATCTCAGGAAGGATCAACCTGGAAAGATAAAAAT
AAACTAGGTGGGGTGAGTGTCCAAAAGGTAGAAGTGGGAAGTCCAGCATGGCCCAAGATATGAAGGGAACAAAGACAAAT
GGAAGGAGTCTGAAAGGAAACATGGCAAAAGGATCAAAATTCCAAATCT

Alignment

ORF - retro_amel_559 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.37 %
• Parental protein coverage: 50.9 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  SRDYDRGYDSRLGSGRRAFGSGYRRDDDYRGGG-DRYEDRYDRRDDRSWSSRDDYSRDDYRRDDRGPPQR
          SRDYD.GYDS.L.S......SGY.RD.DYR..G.D..ED.YDR.D....SS.DDYS.DDYR.D.RGP.QR
Retrocopy SRDYD*GYDSGLNSSSSICVSGYNRDNDYRRSG<DHPEDQYDRHDVQLRSSKDDYSGDDYRYDNRGPSQR

Parental  PKLNLKPRSTPKDDDASASTSQSSRAASIFGGAKPVDTAAREREVEERLQKEQEKLQRQLDEPKLERRPR
          .KLNLK..STPK.DD..A.TSQSS.AAS.FG.A.P.D.A.RE.EVE..LQKEQEK...Q.DEP.LE....
Retrocopy TKLNLKLQSTPKEDDSLAGTSQSSQAASMFGAARPIDPAIREQEVEKQLQKEQEKSNHQRDEPELE*QSQ

Parental  ERHPSWRSEETQERERSRTGSESSQTGTSATSGRNA-RRRESE--KSLENEAPSKEEDCHSPTSKPPKSE
          .R.P.W.SE.TQE.E.SRTGS.SSQTGTSA.S...A.R.R..E....LE.E..S..EDCHSPTS...K..
Retrocopy KRYPKWQSEKTQEQEWSRTGSFSSQTGTSAASEVRA<RMRKGENLRNLEKEVLSTAEDCHSPTSNLAKHN

Parental  QPLKVMPAPPPKENAWVKRSSNPPARSQSSD-TEQQSPTSGGGKVLPAQPPEEGPARRADENKVDGVSV-
          Q.LKV...PP.K..AWVK...N..A..QSS....Q......G.KV.PAQ...EG.....D.NK..GVSV.
Retrocopy QLLKVIMSPPLKVDAWVK*NGNSYA*FQSSN>EQQSPTRDAG-KVAPAQTSQEGSTWK-DKNKLGGVSV<

Parental  PKGQSGNSS-RGPGDGGSKDHWKESDRRDGK-KDQDSRS
          PKG.SG.SS..GP...G.KD.WKES.R..GK.KDQ.S.S
Retrocopy PKGRSGKSS<HGPRYEGNKDKWKESERKHGK<KDQNSKS

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Ailuropoda melanoleuca was not studied using RNA-Seq expression data.

ChIP-Seq

Ailuropoda melanoleuca was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_amel_559 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_559 was not experimentally validated.

Homology

Retrocopy orthology:

Ailuropoda melanoleuca 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 11 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012023	2 retrocopies	retro_amel_1107, retro_amel_559 ,
Canis familiaris	ENSCAFG00000007117	2 retrocopies	retro_cfam_1447, retro_cfam_936,
Choloepus hoffmanni	ENSCHOG00000001608	2 retrocopies	retro_chof_1310, retro_chof_366,
Cavia porcellus	ENSCPOG00000005595	3 retrocopies	retro_cpor_278, retro_cpor_752, retro_cpor_937,
Gorilla gorilla	ENSGGOG00000013695	5 retrocopies	retro_ggor_1233, retro_ggor_1263, retro_ggor_1882, retro_ggor_1883, retro_ggor_3024,
Loxodonta africana	ENSLAFG00000009534	1 retrocopy	retro_lafr_294,
Macropus eugenii	ENSMEUG00000012341	2 retrocopies	retro_meug_1054, retro_meug_585,
Macaca mulatta	ENSMMUG00000001062	5 retrocopies	retro_mmul_1428, retro_mmul_2384, retro_mmul_2589, retro_mmul_731, retro_mmul_783,
Mus musculus	ENSMUSG00000058655	1 retrocopy	retro_mmus_3686,
Rattus norvegicus	ENSRNOG00000010103	2 retrocopies	retro_rnor_2467, retro_rnor_2972,
Tarsius syrichta	ENSTSYG00000012880	1 retrocopy	retro_tsyr_452,