RetrogeneDB ID: retro_ptro_1789

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 3:66641151..66641744(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ILF2
• Ensembl ID: ENSPTRG00000001358
• Aliases: None
• Description: None

Sequence

>retro_ptro_1789
GACGAAACTGGCTTGGAAATCAGTTCTTCTGATGCTACAGTGAAGACTGTCATTACAACAGTGCCACCCAGTCTTCCAAA
ACTGGACCCAGAACTCCGTTTGGATATCAAGGTATTGCAGGGTGCCTTAGCAGCCATTCGGCATGCCCGCTGGTTCAAGG
AAAATGGTTCTCAGTTCACAGTTAAAGTTATCATCAGACTACTGAAGGACTTGAGGGTTTCGTTTTGCTGGCTTTGAGCC
CCTCACACCCTGGATCCTAGGCCTACTAAGTCATTATGCTGTGATAACCCCAACAGACAGCCTTTGGCCCTGAACACTGC
ACATAGGTGTTGCTTGCAGATTCTAGGTGCAGGACTGTTCCTGCCAGGGTCCATGGGTATCATGACCCCTGTGAGAGTGG
CAACTTCAGAGTACACACAGTCATGACCCTAGAACAGCAGGACATAGTCTGCTACACAGCCCAGACTCTGGTCTGAATCC
TCTCACATGGTGGCTTTAGGAAGATCCTTGGCCAGGAGGGTGATGCCAGACATCTTACTTCTGAACTATCTACCTGGGAT
GGAGTGATAGTAACACCTTCAGAAAAGGCTTAC

Alignment

ORF - retro_ptro_1789 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.17 %
• Parental protein coverage: 51.03 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  NETGFEISSSDATVKILITTVPPNLRKLDPELHLDIKVLQSALAAIRHARWFEENASQSTVKVLIRLLKD
          .ETG.EISSSDATVK..ITTVPP.L.KLDPEL.LDIKVLQ.ALAAIRHARWF.EN.SQ.TVKV.IRLLKD
Retrocopy DETGLEISSSDATVKTVITTVPPSLPKLDPELRLDIKVLQGALAAIRHARWFKENGSQFTVKVIIRLLKD

Parental  LRI-RFPGFEPLTPWILDLLGHYAVMNNPT-RQPLALNVAYRRCLQILAAGLFLPGSVGIT-DPCESGNF
          LR..RF.GFEPLTPWIL.LL.HYAV...PT.RQPLALN.A.R.CLQIL.AGLFLPGS.GI..DPCESGNF
Retrocopy LRV>RFAGFEPLTPWILGLLSHYAVI-TPT<RQPLALNTAHRCCLQILGAGLFLPGSMGIM<DPCESGNF

Parental  RVHTVMTLEQQDMVCYTAQTLVRILSHGGFRKILGQEGDASYLASEISTWDGVIVTPSEKAY
          RVHTVMTLEQQD.VCYTAQTLV.ILSHGGFRKILGQEGDA..L.SE.STWDGVIVTPSEKAY
Retrocopy RVHTVMTLEQQDIVCYTAQTLV*ILSHGGFRKILGQEGDARHLTSELSTWDGVIVTPSEKAY

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	0.02 RPM	50.10 RPM
SRP007412_cerebellum	0.04 RPM	66.43 RPM
SRP007412_heart	0.03 RPM	36.43 RPM
SRP007412_kidney	0.08 RPM	157.33 RPM
SRP007412_liver	0.00 RPM	55.91 RPM
SRP007412_testis	0.00 RPM	240.06 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1789 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1789 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1789 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2654
Pongo abelii	retro_pabe_2318

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000017530	1 retrocopy	retro_cfam_1358,
Macropus eugenii	ENSMEUG00000003651	1 retrocopy	retro_meug_1174,
Myotis lucifugus	ENSMLUG00000001847	3 retrocopies	retro_mluc_1046, retro_mluc_217, retro_mluc_2402,
Macaca mulatta	ENSMMUG00000008149	1 retrocopy	retro_mmul_1516,
Pan troglodytes	ENSPTRG00000001358	2 retrocopies	retro_ptro_1789 , retro_ptro_963,
Ictidomys tridecemlineatus	ENSSTOG00000000667	1 retrocopy	retro_itri_130,