RetrogeneDB ID: retro_tsyr_452

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_120371:138..1173(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF4B
• Ensembl ID: ENSTSYG00000012880
• Aliases: None
• Description: eukaryotic translation initiation factor 4B [Source:HGNC Symbol;Acc:3285]

Sequence

>retro_tsyr_452
TATCGTGACGGCCCACGGCGGAATATGGATCGGTACGGGGGCCGGGATCACGATGAAGACCGTGGCAGCAGGGACTGTGA
TCGAGGCTCTGATTCCAGGATAGGCAGTGGCAGAAGCACATTTGGTAGCAGGTACCGAAGAGATGACCACTACGGAGGAG
GCGGGGAACTCTATGAAGACCCATATGAAAGGCGGGACGATGGGTCATGGAGCTCCAGGGATGACTTACTCTCGAGATGA
TTCCAGGCGTGATGACAGAGGTCCCCCCCCCAAAGACCCAAACTGAATCTAAAGCCTCGGAGTACTCCTGAGGAAGATGA
TTCCTCTGCTAGCACCTCCCAGGCCAGCCGAGCAGCTTCTATCCTCGGAGGGGCAAAACCTGTTGACACAGCTGCGAGAG
AGAGAAGTGGAGGAGCGGCTTACAGGAAGAGCAGGAGAAACTGCAGCGCCGGCTGGACGAGCCAAAGCTGGAACGGCGGC
CTCGGAAGAGACACCCAAGCTGGCGAAGTGAAGAAATTCAGGGACCGAACGGTCGAGGACAGGAAGTGAGTCATCACAGA
CTGGGGCCTCAGCCACATCTGGCAGAAGGAAGTCAGATCAGGATGCAGGAAGGAGAGAGAGGGAGAAGTCTCTAGAAAAT
GAAACATTCAATAAGGAGGAAGGCTGTCACTCTCCGACTTCTAAACCTCCCAAACCTGATCAGCCCCTCCACCAAAGGAG
AATGTTTGGGTGAAGCGAAGTTCTAACCCTCCCGCTCGATCTCAGAGCTCAGACACAGAGCGGCAGTCCCCTACAAGTGC
TGGGGGGAAAGTAGCTCCAGGTCAGTCATCTGAGGAAGGACCAACTAGGAAAGCAGATGAAAATAAAGTAGATGGGATAA
GTGTCCCAAAAGGCCAAACTGGGATCTCCAGCCGTGGTCCAGAAGATGGAGGAAACAAAGACCACTGGAAGGATTCAGAT
AGGAAAGATGGCAAAGAGGATCAAGACTCCAGATCTGCACCTGAGTCAAAGAAACCCAAGGAAATTCCAGCCTCT

Alignment

ORF - retro_tsyr_452 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.58 %
• Parental protein coverage: 64.01 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  YRDGPRRDMDRYGGRDRYDDRGSRDYDRGYDSRIGSGRRAFGSGYRRDDDYRGGGDRYEDRYERRDDRSW
          YRDGPRR.MDRYGGRD...DRGSRD.DRG.DSRIGSGR..FGS.YRRDD.Y.GGG..YED.YERRDD.SW
Retrocopy YRDGPRRNMDRYGGRDHDEDRGSRDCDRGSDSRIGSGRSTFGSRYRRDDHYGGGGELYEDPYERRDDGSW

Parental  SSRDD-YSR-DDYRRD-DRGPPQRPKLNLKPRSTPKEDDSSASTSQSSRAASIFGGAKPVDTAARER-EV
          SSRDD.YSR.D..R.D..R....RPKLNLKPRSTP.EDDSSASTSQ.SRAASI.GGAKPVDTAARER...
Retrocopy SSRDD>YSRDDSRRDD<QRXXXXRPKLNLKPRSTPEEDDSSASTSQASRAASILGGAKPVDTAARER<KW

Parental  EERLQKEQEKLQRQLDEPKLERRPRERHPSWRSEETQ-ERERSRTGSESSQTGASATSGRNARRRESEKS
          ...LQ.EQEKLQR.LDEPKLERRPR.RHPSWRSEE.Q...ERSRTGSESSQTGASATSGR..........
Retrocopy RSGLQEEQEKLQRRLDEPKLERRPRKRHPSWRSEEIQ<GTERSRTGSESSQTGASATSGRRKSDQDAGRR

Parental  LENETFNKEEDCHSPTSKPPKPDQPLKVMP-APPPKENAWVKRSSNPSTRSQSSDTEQQSPTSAGGKVAP
          ........E..........P....P....P..PP.KEN.WVKRSSNP..RSQSSDTE.QSPTSAGGKVAP
Retrocopy EREKSLENETFNKEEGCHSPTSKPPKPDQP<PPP-KENVWVKRSSNPPARSQSSDTERQSPTSAGGKVAP

Parental  AQPSEEGPTRK-DENKVDGISVPKGQTGNSSRGPGDGGNKDHWKDSDRKDGKKDQDSRSAPEPKKPEEIP
          .Q.SEEGPTRK.DENKVDGISVPKGQTG.SSRGP.DGGNKDHWKDSDRKDGK.DQDSRSAPE.KKP.EIP
Retrocopy GQSSEEGPTRKADENKVDGISVPKGQTGISSRGPEDGGNKDHWKDSDRKDGKEDQDSRSAPESKKPKEIP

Parental  AS
          AS
Retrocopy AS

Legend:

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

Expression

RNA-Seq

Tarsius syrichta was not studied using RNA-Seq expression data.

ChIP-Seq

Tarsius syrichta was not studied using ChIP-Seq data.

EST

Tarsius syrichta was not studied using EST data.

TSS

Tarsius syrichta was not studied using FANTOM5 data.

Lab

retro_tsyr_452 was not experimentally validated.

Homology

Retrocopy orthology:

Tarsius syrichta 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 ,