RetrogeneDB ID: retro_amel_1300

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193168.1:12892..13983(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF4A1
• Ensembl ID: ENSAMEG00000016753
• Aliases: None
• Description: eukaryotic translation initiation factor 4A1 [Source:HGNC Symbol;Acc:3282]

Sequence

>retro_amel_1300
TCTGAGTTCCTTCTCTGTGGTATCTATGCCTGTGGTTCTGAGAAGCCTTCTGCCATCCAGCAGTGAGCCATTCTTCCTTA
TTTCAAGGATTATGATGTGATCACTCAAGCCCAATCTGGGCCTGGATAAACAGCCACGTTTGCCATGCTGATTCTGCAAC
AGATTGAATTGGATCTAAAGGCTACACAGGCCTTTGTCCTGGCACCCAATAGAGAGTTGGCTCAGCAGATACAATAGGTA
GTCATGGCCTTGGAGGATTGCATGGATGCCTCTTGCCTTGAGGGGACCAATGTACATGCTGAAGTCAGAAGCTGTAGATG
GAAGCTCTCCATATCATCGTGGGTACCCCACGTCATGTGTTTGATATGCTTAACTGGAGATACCTGTTTCCCAACTATAT
CAAGATGTTTGTAGTGGATGAAGCCGATGAAATATTAAGCCACGGATTCAAGGACCAGATCTATGACATATTCCAAAAGC
TGAACAGCAACCAGGTGGTTTTGCTGTCAGCTACATTGCCTTCTGATAACTTGAGGTGACCAAAAAGTTCATGAGGGACC
CCATTCAGATTCTGGTCAAAAAAAGAGGAGCTGACCCTGGGGAGGGTATCTGCCAGGTCTATATCAACGTGGAATGAGAA
GAGTGGAAGCTGGACATACTGTGTGACTTGTATGAAACCCTAACCATCACTTAGGCAGTCATATTCATCAACACCTGAGG
GAAGGTTGATTGGCTCACTGAGAAGATGTACACCTGAGACTTCACCATGTCCACCATGCACAGAGATAATGGACCAAATG
GAACAAGATGTTATCATGAGGGAATTCTGCTCTGGCTCTAGCAGAGTTTTGATGACCACAGACTGGCTGGCCAGAGTCAT
TGGTGTACTGCAGGTTTCTTTAATCATCAACTATGACCTTCCCACCAACAGGAAAACTATATCCACAGAATCGGTCACGG
TGGACAGATATGGCTATAAGGGTGTGGCTATTAACATGGTGACAGAAGAAGAAAAGAGGACTCTTCAAGATGTTGAAACC
TTCTACAACACCTTCATTGAGGAGATGCCTCTCAGTGTTGCTGACCTCATT

Alignment

ORF - retro_amel_1300 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.55 %
• Parental protein coverage: 90.39 %
• Number of stop codons detected: 8
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  SESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQIELDLKATQALVLAPT
          SE.LL.GIYA.G.EKPSAIQQ.AILP..K.YDVI.QAQSG.G.TATFA..ILQQIELDLKATQA.VLAP.
Retrocopy SEFLLCGIYACGSEKPSAIQQ*AILPYFKDYDVITQAQSGPG*TATFAMLILQQIELDLKATQAFVLAPN

Parental  RELAQQIQKVVMALGDYMGASCHACIGGTNVRAEV-QKLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKM
          RELAQQIQ.VVMAL.D.M.AS...C..GTNV.AEV.QKL.MEA.HIIVGTP..VFDMLN.RYL.P.YIKM
Retrocopy RELAQQIQ*VVMALEDCMDAS---CLEGTNVHAEV<QKL*MEALHIIVGTPRHVFDMLNWRYLFPNYIKM

Parental  FVLDEADEMLSRGFKDQIYDIFQKLNSNTQVVLLSATMPSDVL-EVTKKFMRDPIRILVKKEELTL-EGI
          FV.DEADE.LS.GFKDQIYDIFQKLNSN.QVVLLSAT.PSD.L.EVTKKFMRDPI.ILVKK......EGI
Retrocopy FVVDEADEILSHGFKDQIYDIFQKLNSN-QVVLLSATLPSDNL<EVTKKFMRDPIQILVKKRGADPGEGI

Parental  RQFYINVEREEWKLDTLCDLYETLTITQAVIFINTRRKVDWLTEKMHARDFTVSAMHGD-MDQKERDVIM
          .Q.YINVE.EEWKLD.LCDLYETLTIT.AVIFINT..KVDWLTEKM...DFT.S.MH.D.MDQ.E.DVIM
Retrocopy CQVYINVE*EEWKLDILCDLYETLTIT*AVIFINT*GKVDWLTEKMYT*DFTMSTMHRD>MDQMEQDVIM

Parental  REFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTNR-ENYIHRIGRGG-RFGRKGVAINMVTEEDKRT
          REF.SGSSRVL.TTD.LAR.I.V.QVSL.INYDLPTNR.ENYIHRIG.GG.R.G.KGVAINMVTEE.KRT
Retrocopy REFCSGSSRVLMTTDWLARVIGVLQVSLIINYDLPTNR<ENYIHRIGHGG>RYGYKGVAINMVTEEEKRT

Parental  LRDIETFYNTSIEEMPLNVADLI
          L.D.ETFYNT.IEEMPL.VADLI
Retrocopy LQDVETFYNTFIEEMPLSVADLI

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_1300 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1300 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 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016753	1 retrocopy	retro_amel_1300 ,
Callithrix jacchus	ENSCJAG00000015114	8 retrocopies	retro_cjac_1876, retro_cjac_2046, retro_cjac_2521, retro_cjac_2679, retro_cjac_3086, retro_cjac_3203, retro_cjac_395, retro_cjac_727,
Dipodomys ordii	ENSDORG00000014225	1 retrocopy	retro_dord_732,
Macropus eugenii	ENSMEUG00000010780	2 retrocopies	retro_meug_158, retro_meug_179,
Microcebus murinus	ENSMICG00000014759	2 retrocopies	retro_mmur_1164, retro_mmur_1477,
Myotis lucifugus	ENSMLUG00000003415	3 retrocopies	retro_mluc_1047, retro_mluc_1229, retro_mluc_1805,
Macaca mulatta	ENSMMUG00000013499	1 retrocopy	retro_mmul_1280,
Monodelphis domestica	ENSMODG00000007090	3 retrocopies	retro_mdom_1282, retro_mdom_326, retro_mdom_711,
Otolemur garnettii	ENSOGAG00000008132	2 retrocopies	retro_ogar_1375, retro_ogar_1862,
Ochotona princeps	ENSOPRG00000008591	2 retrocopies	retro_opri_155, retro_opri_985,
Sorex araneus	ENSSARG00000006017	7 retrocopies	retro_sara_224, retro_sara_383, retro_sara_461, retro_sara_567, retro_sara_6, retro_sara_605, retro_sara_89,