RetrogeneDB ID: retro_pabe_2318

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 3:80264547..80265141(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ILF2
• Ensembl ID: ENSPPYG00000000800
• Aliases: None
• Description: Interleukin enhancer-binding factor 2 [Source:UniProtKB/Swiss-Prot;Acc:Q5RFJ1]

Sequence

>retro_pabe_2318
AACGAAACTGGCTTGGAAATCAGTTCTTCTGATGCTACAGTGAAGACTGTCATTACAACAGCGCCACCCAGTCTTCCAAA
ACTGGACCCAGAACTCCATTTGGATATCAAGGTACTGCAGGGTACCTTAGCAGCCATTCGGCATGCCCGCTGGTTCAAGG
AAAATGGTTCTCAGTTCACAGTTAAAGTTATCATCAGACTACTGAAGGACTTGAGGGTTTCGTTTTCCTGGCTTTGAGCC
CCTCACGCCCTGGATCCTAGGCCTACTAAGTCATTATGCTGTGATAACCCCAACAGACAGCCTTTAGCCCTGAACACTGC
ACACAGGTGTTGCTTGCAGATTCTAGGTGCAGGACTTTTCCTGCCAGGGTCCATGGGTATCACTGACCCCTGTGAGAGTG
GCAACTTCAGAGTACACACAGTCATGGCCCTAGAACAGCAGGACATAGTCTGCTACACAGCCCAGACTCTGGTCTGAATC
CTGTCACATGGTGACTTTAGGAAGATCCTTGGCCAGGAGGGTGATGCCAGCCATCTTGCTTCTGAAATATCTACCTGGGA
TGGAGTGATAGTAACACCTTCAGAAAAGGCTTAC

Alignment

ORF - retro_pabe_2318 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.07 %
• Parental protein coverage: 51.03 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NETGFEISSSDATVKILITTVPPNLRKLDPELHLDIKVLQSALAAIRHARWFEENASQSTVKVLIRLLKD
          NETG.EISSSDATVK..ITT.PP.L.KLDPELHLDIKVLQ..LAAIRHARWF.EN.SQ.TVKV.IRLLKD
Retrocopy NETGLEISSSDATVKTVITTAPPSLPKLDPELHLDIKVLQGTLAAIRHARWFKENGSQFTVKVIIRLLKD

Parental  LRI-RFPGFEPLTPWILDLLGHYAVMNNPT-RQPLALNVAYRRCLQILAAGLFLPGSVGITDPCESGNFR
          LR..RFPGFEPLTPWIL.LL.HYAV...PT.RQPLALN.A.R.CLQIL.AGLFLPGS.GITDPCESGNFR
Retrocopy LRV>RFPGFEPLTPWILGLLSHYAVI-TPT<RQPLALNTAHRCCLQILGAGLFLPGSMGITDPCESGNFR

Parental  VHTVMTLEQQDMVCYTAQTLVRILSHGGFRKILGQEGDASYLASEISTWDGVIVTPSEKAY
          VHTVM.LEQQD.VCYTAQTLV.ILSHG.FRKILGQEGDAS.LASEISTWDGVIVTPSEKAY
Retrocopy VHTVMALEQQDIVCYTAQTLV*ILSHGDFRKILGQEGDASHLASEISTWDGVIVTPSEKAY

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	0.00 RPM	68.28 RPM
SRP007412_cerebellum	0.12 RPM	65.79 RPM
SRP007412_heart	0.12 RPM	28.45 RPM
SRP007412_kidney	0.00 RPM	169.15 RPM
SRP007412_liver	0.00 RPM	44.49 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2318 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2318 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2318 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2654
Pan troglodytes	retro_ptro_1789

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000143621	2 retrocopies	retro_hsap_1405, retro_hsap_2654,
Macropus eugenii	ENSMEUG00000003651	1 retrocopy	retro_meug_1174,
Microcebus murinus	ENSMICG00000013730	1 retrocopy	retro_mmur_206,
Myotis lucifugus	ENSMLUG00000001847	3 retrocopies	retro_mluc_1046, retro_mluc_217, retro_mluc_2402,
Oryctolagus cuniculus	ENSOCUG00000005430	1 retrocopy	retro_ocun_1216,
Pongo abelii	ENSPPYG00000000800	1 retrocopy	retro_pabe_2318 ,
Ictidomys tridecemlineatus	ENSSTOG00000000667	1 retrocopy	retro_itri_130,
Tarsius syrichta	ENSTSYG00000012061	3 retrocopies	retro_tsyr_1448, retro_tsyr_1745, retro_tsyr_496,