RetrogeneDB ID: retro_itri_1707

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393647.1:39290..40030(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MLF2
• Ensembl ID: ENSSTOG00000009908
• Aliases: None
• Description: myeloid leukemia factor 2 [Source:HGNC Symbol;Acc:7126]

Sequence

>retro_itri_1707
ATGTTCTGCTTCATGAGGGACGTGGAGCCTGAGGATCCCATGTTCCTGATCGACCCCTTTGCTATTCACCGTCAGCATAT
GAGCCGCATGTTGTCAGGTGGCTTTGGTTATAGCCCCTTCCTTAGCATCACAGATGGCAACATGCCAGGGACCAGGCCTG
CCAGCCGCAGGATGCAGCCTGGGGCTGTCTACCCCTTTGGGATGCTGGGAATGTCGGGTGGCTTCATGGACATGTTTGGG
ATGATGAATGACATGATTGGGAATATGGAGCATATGACAGCTGGGGGCAATTGCCAGACCTTTTCATCCTCTACTGTCAT
CTCCTACTCCAATACTGGTGATGGTGCCCCCAAGGTCTATCAGGAGACATCAGAGATGCGCTCAGCACCAGGCGGGATCC
GGCAGATACGGAGGACTGTCCGCGACTCAGACAGTGGACTAGAGCAGATGTCCATTGGGCATCACATCTGAGACAGGGCT
CACATCCTCCAGCCTTCCCGAAATCACCGCACAGGAGACCAGGAGGAACAGCAGGACTATATCAACCTGGATGAGAGTGA
GGCAGCAGCATTTGGTGATGAGTGGCGAAGAGAGACATCCAGATTCCGGCAGCAGCGCCCTCTGGAATTTCGAAGGCATG
AGGCATTTGTGAGTGGGGGTCGAAGGGCCGAGGGGCCTCCCCGCCTGGCCATCCAGGGACTGAGGACTCCCCCTCCCGAC
AGTCCCGCCGCTATGACTGG

Alignment

ORF - retro_itri_1707 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.35 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MFRFMRDVEPEDPMFLMDPFAIHRQHMSRMLSGGFGYSPFLSITDGNMPGTRPASRRMQAGAVSPFGMLG
          MF.FMRDVEPEDPMFL.DPFAIHRQHMSRMLSGGFGYSPFLSITDGNMPGTRPASRRMQ.GAV.PFGMLG
Retrocopy MFCFMRDVEPEDPMFLIDPFAIHRQHMSRMLSGGFGYSPFLSITDGNMPGTRPASRRMQPGAVYPFGMLG

Parental  MSGGFMDMFGMMNDMIGNMEHMTAGGNCQTFSSSTVISYSNTGDGAPKVYQETSEMRSAPGGIRETRRTV
          MSGGFMDMFGMMNDMIGNMEHMTAGGNCQTFSSSTVISYSNTGDGAPKVYQETSEMRSAPGGIR..RRTV
Retrocopy MSGGFMDMFGMMNDMIGNMEHMTAGGNCQTFSSSTVISYSNTGDGAPKVYQETSEMRSAPGGIRQIRRTV

Parental  RDSDSGLEQMSIGHHIRDRAHILQRSRNHRTGDQEERQDYINLDESEAAAFDDEWRRETSRFRQQRPLEF
          RDSDSGLEQMSIGHHI.DRAHILQ.SRNHRTGDQEE.QDYINLDESEAAAF.DEWRRETSRFRQQRPLEF
Retrocopy RDSDSGLEQMSIGHHI*DRAHILQPSRNHRTGDQEEQQDYINLDESEAAAFGDEWRRETSRFRQQRPLEF

Parental  RRHEASVSGGRRTEGPPRLAIQ-GPEDSPSRQSRRYDW
          RRHEA.VSGGRR.EGPPRLAIQ.G.EDSPSRQSRRYDW
Retrocopy RRHEAFVSGGRRAEGPPRLAIQ<GTEDSPSRQSRRYDW

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_1707 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1707 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 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000000758	2 retrocopies	retro_dnov_1602, retro_dnov_649,
Echinops telfairi	ENSETEG00000014471	2 retrocopies	retro_etel_1236, retro_etel_233,
Microcebus murinus	ENSMICG00000010652	1 retrocopy	retro_mmur_449,
Monodelphis domestica	ENSMODG00000018113	1 retrocopy	retro_mdom_324,
Mus musculus	ENSMUSG00000030120	1 retrocopy	retro_mmus_1090,
Otolemur garnettii	ENSOGAG00000005976	1 retrocopy	retro_ogar_232,
Procavia capensis	ENSPCAG00000001026	1 retrocopy	retro_pcap_326,
Ictidomys tridecemlineatus	ENSSTOG00000009908	1 retrocopy	retro_itri_1707 ,