RetrogeneDB ID: retro_cfam_1358

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 3:83910464..83911326(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ILF2
• Ensembl ID: ENSCAFG00000017530
• Aliases: None
• Description: interleukin enhancer binding factor 2 [Source:HGNC Symbol;Acc:6037]

Sequence

>retro_cfam_1358
ATCCTTTCTCTGGTGACAAAAATCAACAATGTGACTGACAATTTGATTGTGGCTCCAGGGACATTCGAAGAGCAAACTGA
AGAAGTGTGACAGGTGGGATCGTATAAAAAGGGAACAATGACTACAGGACACAATGTGGTGGTAATCCTAAAGATTCTGC
CAACATTGGAAGCTGCTGCCGCCCTAGGGAACGAAGTTGTGGAAAGCCTGAGAGCACAGGATCCTTCTGAAGTTTTAACC
ATGCTGACCAACGAAACTGGCTTTGAGATCAGTTCTTCTGATGCTACAGTGAAGATTCTCATTACAACAGTGCCACCCAA
TCTCCGAAAACTGGACCCAGAACTCCATTTGGATATCAGGGGGTTGCAGAGTGCTTCAGCAGCCATCAGACATGCCTGCT
GGTTTGAGGAAAATGCTTCTCAGTCCACAGTTAAAGTTCTCATTAGACTGCTGAGAACCTGTGGATTCGTTTTCCTGGCT
TTGAGCCACTAACACCCTGGATCCTTGACCTACTCGGGCACTATACTGTGATGAACAATCCCACCAGACAGCCTTTGGCC
CTAAATGTGGCATACAGGCGGTGCTTACAGATTCTGGCTGCAGGACTGTTCCTGCCAGGGTCAGTGGGAATCACTGACCC
CTGTGAAAGTGGCAACTTCAGAGTACACACAGTCATGACTCTGGAACAACAGGACATGGTGCGCTATACAGCTCAGATTC
TGGTCCGTATCCTCTCACATGATGGTTTTCGGAAGATTCTTGGCCAGGAGGGTGATGCCAGCTATCTTGCTTCTGAGATA
TCTACCTGGGATGGAGTGATAGTGACACCTTCAGAAAAGGCTATGGGAAGCCACCAGAAAAG

Alignment

ORF - retro_cfam_1358 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.15 %
• Parental protein coverage: 74.62 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ILSLVTKINNVIDNLIVAPGTFEVQIEEVRQVGSYKKGTMTTGHNVADLVVILKILPTLEAVAALGNKVV
          ILSLVTKINNV.DNLIVAPGTFE.Q.EEV.QVGSYKKGTMTTGHNV...VVILKILPTLEA.AALGN.VV
Retrocopy ILSLVTKINNVTDNLIVAPGTFEEQTEEV*QVGSYKKGTMTTGHNV---VVILKILPTLEAAAALGNEVV

Parental  ESLRAQDPSEVLTMLTNETGFEISSSDATVKILITTVPPNLRKLDPELHLDIKVLQSALAAIRHARWFEE
          ESLRAQDPSEVLTMLTNETGFEISSSDATVKILITTVPPNLRKLDPELHLDI..LQSA.AAIRHA.WFEE
Retrocopy ESLRAQDPSEVLTMLTNETGFEISSSDATVKILITTVPPNLRKLDPELHLDIRGLQSASAAIRHACWFEE

Parental  NASQSTVKVLIRLLK-DLRIRFPGFEPLTPWILDLLGHYAVMNNPTRQPLALNVAYRRCLQILAAGLFLP
          NASQSTVKVLIRLL...L.IRFPGFEPLTPWILDLLGHY.VMNNPTRQPLALNVAYRRCLQILAAGLFLP
Retrocopy NASQSTVKVLIRLLR<NLWIRFPGFEPLTPWILDLLGHYTVMNNPTRQPLALNVAYRRCLQILAAGLFLP

Parental  GSVGITDPCESGNFRVHTVMTLEQQDMVCYTAQTLVRILSHGGFRKILGQEGDASYLASEISTWDGVIVT
          GSVGITDPCESGNFRVHTVMTLEQQDMV.YTAQ.LVRILSH.GFRKILGQEGDASYLASEISTWDGVIVT
Retrocopy GSVGITDPCESGNFRVHTVMTLEQQDMVRYTAQILVRILSHDGFRKILGQEGDASYLASEISTWDGVIVT

Parental  PSEKA-YEKPPEK
          PSEKA.Y.KPPEK
Retrocopy PSEKA<YGKPPEK

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
SRP012049_cerebellum	0.00 RPM	107.35 RPM
SRP017611_brain	0.00 RPM	55.65 RPM
SRP017611_kidney	0.00 RPM	83.21 RPM
SRP017611_liver	0.00 RPM	20.74 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1358 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1358 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1358 has 0 orthologous retrocopies within eutheria group .

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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,