RetrogeneDB ID: retro_itri_130

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393374.1:4999075..5000221(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000021457
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: ILF2
• Ensembl ID: ENSSTOG00000000667
• Aliases: None
• Description: interleukin enhancer binding factor 2 [Source:HGNC Symbol;Acc:6037]

Sequence

>retro_itri_130
NGTGGGCGCTTTGGTTCCAGAGGGGGACCAGGAGGAGGGTTCAGGCCCTTCGTGCCACATATCCCATTCGATTTCTATTT
GTGTGAAATGGCCTTCCCTCGAGTCAAGGCAGCACCTGATGAAACTTCCTTCAGTGAAGCCTTGCTGAAGAGGAATCAGG
ACCTTGCTCCCAATTCTGCTGAACAGGCCTCAATCCTTTCTCTGGTGACAAAAATAAACAATGTGATCGACAATTTGATT
GTGGCTCCAGGGACATTTGAAGTGCAAATTGAAGAAGTCCGACAGGTAGGATCATATAAAAAGGGAACAATGACTACAGG
ACACAACGTAGCTGACCTGGTGGTAATACTAAAGATTCTGCCAACATTGGAAGCTGTTGCTGCCCTGGGGAACAAAGTCG
TGGAAAGTTTAAGAGCACAGGATCCATCTGAAGTTTTGACCATGCTGACCAATGAAACTGGTTTTGAAATCAGTTCTTCT
GATGCGACAGTGAAGATTCTCATTACGACAGTGCCACCCAATCTCCGAAAACTGGACCCGGAACTCCACTTGGATATCAA
GGTGTTGCAGAGTACTTTAGCAGCCATCCGACATACCCGCTGGTTTGAGGAAAATGCTTCTCAGTCCACAGTTAAAGTTC
TCATCAGACTGCTGAAGGACTTAAGGATTCGTTTTCCTGGCTTTGAGCCCCTCACACCCTGGATCCTTGACCTACTTGGG
CACTATGCGGTGATGAATAACCCCACCAGACAGCCTTTGGCCCTAAATGTGGCATACAGGCGTTGCTTGCAGATTCTGGC
TGCAGGACTGTTTCTTCCAGGATCAGTGGGTATCACTGACCCCTGTGAAAATGGCAACTTCAGAGTACATACGGTCATGA
CCCTGGAACAGCAGGATATGGTCTGCTACACAGCTCAGACTCTGGTTCGAATCCTCTCACACGGTGGCTTTAGGAAGATC
CTTGGCCAGGAGGGTGATGCCAGCTATCTTGCTTCTGAAATATCTACCTGGGATGGAGTGATAGTGACACCTTCAGAAAA
GGCTTACGAGAAGCCACCTGAGAAGAAGGAAGGAGAGGAAGAGGAGGAGAATACAGAAGAACCACCTCAAGGAGAGGAAG
AGGAAAGCATGGAAACTCAAGAGTGA

Alignment

ORF - retro_itri_130 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.95 %
• Parental protein coverage: 97.44 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GRFGSRGGPGGGFRPFVPHIPFDFYLCEMAFPRVKPAPDETSFSEALLKRNQDLAPNSAEQASILSLVTK
          GRFGSRGGPGGGFRPFVPHIPFDFYLCEMAFPRVK.APDETSFSEALLKRNQDLAPNSAEQASILSLVTK
Retrocopy GRFGSRGGPGGGFRPFVPHIPFDFYLCEMAFPRVKAAPDETSFSEALLKRNQDLAPNSAEQASILSLVTK

Parental  INNVIDNLIVAPGTFEVQIEEVRQVGSYKKGTMTTGHNVADLVVILKILPTLEAVAALGNKVVESLRAQD
          INNVIDNLIVAPGTFEVQIEEVRQVGSYKKGTMTTGHNVADLVVILKILPTLEAVAALGNKVVESLRAQD
Retrocopy INNVIDNLIVAPGTFEVQIEEVRQVGSYKKGTMTTGHNVADLVVILKILPTLEAVAALGNKVVESLRAQD

Parental  PSEVLTMLTNETGFEISSSDATVKILITTVPPNLRKLDPELHLDIKVLQSALAAIRHARWFEENASQSTV
          PSEVLTMLTNETGFEISSSDATVKILITTVPPNLRKLDPELHLDIKVLQS.LAAIRH.RWFEENASQSTV
Retrocopy PSEVLTMLTNETGFEISSSDATVKILITTVPPNLRKLDPELHLDIKVLQSTLAAIRHTRWFEENASQSTV

Parental  KVLIRLLKDLRIRFPGFEPLTPWILDLLGHYAVMNNPTRQPLALNVAYRRCLQILAAGLFLPGSVGITDP
          KVLIRLLKDLRIRFPGFEPLTPWILDLLGHYAVMNNPTRQPLALNVAYRRCLQILAAGLFLPGSVGITDP
Retrocopy KVLIRLLKDLRIRFPGFEPLTPWILDLLGHYAVMNNPTRQPLALNVAYRRCLQILAAGLFLPGSVGITDP

Parental  CESGNFRVHTVMTLEQQDMVCYTAQTLVRILSHGGFRKILGQEGDASYLASEISTWDGVIVTPSEKAYEK
          CE.GNFRVHTVMTLEQQDMVCYTAQTLVRILSHGGFRKILGQEGDASYLASEISTWDGVIVTPSEKAYEK
Retrocopy CENGNFRVHTVMTLEQQDMVCYTAQTLVRILSHGGFRKILGQEGDASYLASEISTWDGVIVTPSEKAYEK

Parental  PPEKKEGEEEEENTEEPPQGEEEESMETQE
          PPEKKEGEEEEENTEEPPQGEEEESMETQE
Retrocopy PPEKKEGEEEEENTEEPPQGEEEESMETQE

Legend:

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

Expression

RNA-Seq

Ictidomys tridecemlineatus was not studied using RNA-Seq expression data.

ChIP-Seq

Ictidomys tridecemlineatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_itri_130 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_130 was not experimentally validated.

Homology

Retrocopy orthology:

Ictidomys tridecemlineatus 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 12 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000017530	1 retrocopy	retro_cfam_1358,
Erinaceus europaeus	ENSEEUG00000013100	1 retrocopy	retro_eeur_500,
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,
Macaca mulatta	ENSMMUG00000008149	1 retrocopy	retro_mmul_1516,
Oryctolagus cuniculus	ENSOCUG00000005430	1 retrocopy	retro_ocun_1216,
Pongo abelii	ENSPPYG00000000800	1 retrocopy	retro_pabe_2318,
Pan troglodytes	ENSPTRG00000001358	2 retrocopies	retro_ptro_1789, retro_ptro_963,
Ictidomys tridecemlineatus	ENSSTOG00000000667	1 retrocopy	retro_itri_130 ,
Tarsius syrichta	ENSTSYG00000012061	3 retrocopies	retro_tsyr_1448, retro_tsyr_1745, retro_tsyr_496,