RetrogeneDB ID: retro_ocun_1216

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 3:146305382..146306323(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ILF2
• Ensembl ID: ENSOCUG00000005430
• Aliases: None
• Description: interleukin enhancer binding factor 2 [Source:HGNC Symbol;Acc:6037]

Sequence

>retro_ocun_1216
TCTGTGGTGACAAAAATAAACAATGTGATTGACAATTTGATTGTATCTCCAGGGACATTTGAAGTGCAAATTGAAGAAGT
CCGGCAGGCATGATCTTATATAAAGGGAACCATGACTACAGGACACAATGTGGCTGACCCGGTGGTGATATTCAAGATCC
TGCCAACATTGGAAGCTGTTACTGACCTGGGGAACAAAGTCGTGGAAAGCCTGAGAGCACAGAATCCTTTGGAAGTTTTG
ACCACGCTGACCAATGAAATTGGCTTTGAAATCAGTTCTTCGGGTGCCACGGTGAAGATTCTGATTACCACAGTGCTGCC
TAATCTCCGAAAACTGAACCCAGAATTCCACTTGGATATCAAGGTGTTGCAGAGTGCCTTAGCAACCATCCGACACGCCC
TCTGGTTTGAGGAAAATGCCTCTCAGTCCACTAAGTTCTCATTAGACTGCTGAAGGACTTGAGGATTCGTTTTCCCAGCT
TTGAGCCCCTCACACCCTGGATCCTTGATCTGCTTGGGCACTGCGCCATGATAAACAACCCCATGAGACAGCCTCCGGCC
CTAAACGTGGCATACAGGCGATGCTTGCAGATTCTGGCTGCAGGACTGTTCCTTCCAGGTTCCGTGGGTATCACTGACCC
CTGTGAGAGTGGCAACTTCAGAGTGCACACAGTCCTGACCCTGGAGCAGCAGGACATGGTGCGCTACACAGCTCAGACTC
TGGTGTGAATGCTCTCGCCCGGGGGCTCTACGAAGATCCTCGGCCAGGAGGGGGACACGAGCTATCTTGCTTCTGAAATG
TCTACCTGGGACGGAGCGATAGTGACTCCTTCAGAAAAGGCTTATGAGAAGCCACCAGAGAAGAAGGAAGGTGAGGAAGA
GGAGGAGAACACCAAAGAACCACCTCAAGGAGAGGAAGAGGAACGCATGGAGACTCAGGAG

Alignment

ORF - retro_ocun_1216 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.44 %
• Parental protein coverage: 77.4 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SLVTKINNVIDNLIVAPGTFEVQIEEVRQVGSYKKGTMTTGHNVADLVVILKILPTLEAVAALGNKVVES
          S.VTKINNVIDNLIV.PGTFEVQIEEVRQ..SY.KGTMTTGHNVAD.VVI.KILPTLEAV..LGNKVVES
Retrocopy SVVTKINNVIDNLIVSPGTFEVQIEEVRQA*SYIKGTMTTGHNVADPVVIFKILPTLEAVTDLGNKVVES

Parental  LRAQDPSEVLTMLTNETGFEISSSDATVKILITTVPPNLRKLDPELHLDIKVLQSALAAIRHARWFEENA
          LRAQ.P.EVLT.LTNE.GFEISSS.ATVKILITTV.PNLRKL.PE.HLDIKVLQSALA.IRHA.WF.E..
Retrocopy LRAQNPLEVLTTLTNEIGFEISSSGATVKILITTVLPNLRKLNPEFHLDIKVLQSALATIRHALWF-EEN

Parental  SQSTVK-VLIRLLKDLRIRFPGFEPLTPWILDLLGHYAVMNNPTRQPLALNVAYRRCLQILAAGLFLPGS
          .....K.VLIRLLKDLRIRFP.FEPLTPWILDLLGH.A..NNP.RQP.ALNVAYRRCLQILAAGLFLPGS
Retrocopy ASQSTK<VLIRLLKDLRIRFPSFEPLTPWILDLLGHCAMINNPMRQPPALNVAYRRCLQILAAGLFLPGS

Parental  VGITDPCESGNFRVHTVMTLEQQDMVCYTAQTLVRILSHGGFRKILGQEGDASYLASEISTWDGVIVTPS
          VGITDPCESGNFRVHTV.TLEQQDMV.YTAQTLV..LS.GG..KILGQEGD.SYLASE.STWDG.IVTPS
Retrocopy VGITDPCESGNFRVHTVLTLEQQDMVRYTAQTLV*MLSPGGSTKILGQEGDTSYLASEMSTWDGAIVTPS

Parental  EKAYEKPPEKKEGEEEEENTEEPPQGEEEESMETQE
          EKAYEKPPEKKEGEEEEENT.EPPQGEEEE.METQE
Retrocopy EKAYEKPPEKKEGEEEEENTKEPPQGEEEERMETQE

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
SRP017611_brain	0.00 RPM	125.39 RPM
SRP017611_kidney	0.00 RPM	129.84 RPM
SRP017611_liver	0.00 RPM	41.39 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1216 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1216 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1216 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 10 parental genes, and 15 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 ,
Oryctolagus cuniculus	ENSOCUG00000013990	1 retrocopy	retro_ocun_1648,
Oryctolagus cuniculus	ENSOCUG00000016737	1 retrocopy	retro_ocun_1813,
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,