RetrogeneDB ID: retro_amel_1107

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192908.1:978833..979870(+)
• 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_1107
CAGGATAAAGGCAGGAATGATCATTCTTCTGGTGGAGATAGAAATCAGGATTTTGACAAAATAGATACACACTGGAGGGC
CCATCTTGCGACAGACAGCTTTGATGCCTACCTGCCTAGAAGAGGTGATGATAGTTTTGGAGACAAGTGCAAGATCATTA
TGATTCTGGCCAATATCATAATGGGCATTGGGATGTGGTACCATGATGGCCCACACCACGATATGGATTGATATGGGGGC
TGGGATCACTGTGATGACTGAAGCAGCAGAGGCTATGACAGAGGCAATGATTCCAGGATAGGCAGTGGCAGAAGAGCATT
TGGCAGTGGGTACCATAGGGATGGTGTATACAGAGGAGGAAGGGACCGCTATGAAGACAGATATGACAGAAGAGATGATT
GGTCATGGAGCTCCAGCAATGATTACTCTCAGGATGATTATAGGCATGTTGATAGAGGTGTCTCCAACAAACCAAGTCTA
AAGCCTTGGAGTACTTCCAAGGAGGATGGTTCCTCTGCTAGCACCTCACAGACCATTCGAGCAGCCTGTCGATGGAGGGT
CAAAGACTGTTGACACAGTGCTAAAGAAGGAAAAGTAGAAAAGTAGCTACAGAAGGGACAGGGGAGAGAAGGAACAGAGG
AGCGTCAGCTGGATGAAGCAAAACTAGAATGTCAACCTTGGGAGAGATTCCAAGCTGATGAAGTAAAGAAACTCAAGAAA
GGGAATGGTTGAGGACAGGAAGTGAGTCACCTCAGGCTGGGACCTCAACCCCATCTGGCAGAAGTGCACCAAGGAGAGAG
CATGAGAAGTCTCTAGAAAATGAAACACTCAATTAAGAGGAAGACTGTCACTCTCCAACTTCTAAACCTCCCAAACCTGA
ACAGCCTCTAAAAGTAATGCCAGGCCCTCCACCAAAGCAGAATGCTTGGGTGCAGCAAAGTTCTAGCCGTCCTGTTGGAT
CTCAGGGCTCAGACACAGAGCAGCAACCCCCTGTAGGGGGTGGGGTAGTTCCTGCTCAGCCATCCAAGAAAGGACCA

Alignment

ORF - retro_amel_1107 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.48 %
• Parental protein coverage: 56.96 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  QDKDRDDRSFGRDRNRDSDKTDTDWRARPATDSFDDYPPRRGDDSFGDKYR-DRYDSDRYRDGYRD-GYR
          QDK.R.D.S.G.DRN.D.DK.DT.WRA..ATDSFD.Y.PRRGDDSFGDK...D.YDS..Y..G..D..Y.
Retrocopy QDKGRNDHSSGGDRNQDFDKIDTHWRAHLATDSFDAYLPRRGDDSFGDKCK<DHYDSGQYHNGHWD>WYH

Parental  DGPRRDMDRYGGRDRYDDRGSRDYDRGYDSRLGSGRRAFGSGYRRDDDYRGGGDRYEDRYDRRDDRSWSS
          DGP..DMD.YGG.D..DD..SR.YDRG.DSR.GSGRRAFGSGY.RD..YRGG.DRYEDRYDRRDD.SWSS
Retrocopy DGPHHDMD*YGGWDHCDD*SSRGYDRGNDSRIGSGRRAFGSGYHRDGVYRGGRDRYEDRYDRRDDWSWSS

Parental  RDDYSRDDYRRDDRGPPQRPKLNLKPRSTPKDDDASASTSQSSRAAS-IFGGAKPVDT-AAREREVEERL
          ..DYS.DDYR..DRG....P...LKP.ST.K.D..S.........A....GG.K.VDT..A.E..VE..L
Retrocopy SNDYSQDDYRHVDRGVSNKP--SLKPWSTSKED-GSSASTSQTIRAA>VDGGSKTVDT<SAKEGKVEK*L

Parental  QKEQEKL---QRQLDEPKLERRPRERH-PSWRSEETQERERSRTGSESSQTGTSATSGRNARRRESEKSL
          QK.Q.......RQLDE.KLE..P.ER..PS..S.ETQERE..RTGSES.Q.GTS..SGR.A.RRE.EKSL
Retrocopy QKGQGREGTEERQLDEAKLECQPWERF<PS**SKETQEREWLRTGSESPQAGTSTPSGRSAPRREHEKSL

Parental  ENEAPSKEEDCHSPTSKPPKSEQPLKVMPAPPPKENAWVKRSSNPPARSQSSDTEQQSPTSGGGKVLPAQ
          ENE....EEDCHSPTSKPPK.EQPLKVMP.PPPK.NAWV..SS..P..SQ.SDTEQQ.P..GG..V.PAQ
Retrocopy ENETLN*EEDCHSPTSKPPKPEQPLKVMPGPPPKQNAWVQQSSSRPVGSQGSDTEQQPPVGGG--VVPAQ

Parental  PPEEGP
          P...GP
Retrocopy PSKKGP

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_1107 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1107 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.

---

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,