RetrogeneDB ID: retro_itri_80

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393759.1:198453..199560(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000013716
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000026874
• Aliases: None
• Description: None

Sequence

>retro_itri_80
ATGTTCTCATTGCCCCGCGGCTTCGAGCCCCAAGCTCCAGAGGACTTGGGGCAGCGGAGTTCGGCAGAGCTGGGGGAGAT
GTTGAAGCGCCAGGAGAGACTTTTGCGCAACGAAAAATTCATTTGCAGATTGCCCGACAAAGGTAAAAAGATCTTAGACA
CTGTTGCCAAACTGAAAGCTGCCACTGCAGAGCGTGAGGAGGTTAGAGGAAAACGTGAACTGTTTCGTTCTGCTAGTTTA
GACTGTGAGGTAAGGCAAAAAGTAACTGCAGGAGTTGATGTGGATATGGAAAAGGCCCAGAGTTCTGACCGAATACTTGA
TACTTCATCACCAGTTCATGCCTGTTCCTTTGTAGATAACATCAAATCATCTAACACAACCTCAGAAAAACAGGGACTTG
TACATCCTACTCAAAAAGGTGATGAAGAGATTCCAGAGGCTGAGTACACAGTCAACAAGCGCCCAGCCTCCCACAAGAGA
TTCAGGGGATCTTCCTCACTTGAAGCAAGAGAGCATCTCCCTCAGCATTGTGTTTCAAGTCAAGCAGAAGATACTTCCAG
CAGTTTTGACAACCAGTTTATTGATAAGTTCCAAAGGATCACAGTTGCAGACCAAGGTACACATCACTCGGAAGAAAACA
CAAGTGCTGAAAACTTGATGGGCCTTCGTGATAGGACTCCTAAGAAGCCCCATTACCCGGAAGTGTTAGAAATGAGAGCC
AAAAATCCAGTGCCCCCACCACATAAATTTAAAACTAATGTTTTGCCATCACATCGCAATGACTCACCTAGTCATTCTCA
GAGGGGAGAGTCTCCTGTTTCCTTGGCAGAGCAGAGGCGCAGGGACAAGCAGCATCTTGATGACATCACAGCAGCGCGGC
TCCTGCCACTTCACCATCTGCCTGCACAGCTGCTTTCCATAGAAGACTCTTTGGCACTTCAGAAACAGCAGAAACAGAAT
TATGAGGAGATGCAAGCAAAGCTCGCAGCACAAAAATTAGCTGAAAGACTGAATATTAAAATGCAGAGTTATAATCCAGA
AGGGGAGTCTTCAGGGAAGTACCGAGAAGTAAGAGAAGAAGATCAGTCCTCTGATGATGAATTATGA

Alignment

ORF - retro_itri_80 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.4 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MFSLPRGFEPQAPEDLGQRSSAELGEMLKRQERLLRNEKFICRLPDKGKKILDTVAKLKAAIAEREEVRG
          MFSLPRGFEPQAPEDLGQRSSAELGEMLKRQERLLRNEKFICRLPDKGKKILDTVAKLKAA.AEREEVRG
Retrocopy MFSLPRGFEPQAPEDLGQRSSAELGEMLKRQERLLRNEKFICRLPDKGKKILDTVAKLKAATAEREEVRG

Parental  KRELFHSASLDCKLRQKVIAGVDVDREKAQSSDRILDTSSPVHACSFVDNIKSSNTTSEKQGLVHPTQKG
          KRELF.SASLDC..RQKV.AGVDVD.EKAQSSDRILDTSSPVHACSFVDNIKSSNTTSEKQGLVHPTQKG
Retrocopy KRELFRSASLDCEVRQKVTAGVDVDMEKAQSSDRILDTSSPVHACSFVDNIKSSNTTSEKQGLVHPTQKG

Parental  DEEIPEAEYTVNKCPASHNRFRGSSSLEAREHLPQHCVSSQAEDTSSSFDNQFIDKFQRITVADQGIHHS
          DEEIPEAEYTVNK.PASH.RFRGSSSLEAREHLPQHCVSSQAEDTSSSFDNQFIDKFQRITVADQG.HHS
Retrocopy DEEIPEAEYTVNKRPASHKRFRGSSSLEAREHLPQHCVSSQAEDTSSSFDNQFIDKFQRITVADQGTHHS

Parental  EENTSAENLMGLRDRTPKKPHYMEVLEMRAKNPVPPPHKFKTNVLPSHHNDSPSHSQRGESPVSLAERRR
          EENTSAENLMGLRDRTPKKPHY.EVLEMRAKNPVPPPHKFKTNVLPSH.NDSPSHSQRGESPVSLAE.RR
Retrocopy EENTSAENLMGLRDRTPKKPHYPEVLEMRAKNPVPPPHKFKTNVLPSHRNDSPSHSQRGESPVSLAEQRR

Parental  RDKQHLDDITAARLLPLHHLPAQLLSIEDSLALQKQQKQNYEVFRA
          RDKQHLDDITAARLLPLHHLPAQLLSIEDSLALQKQQKQNYE...A
Retrocopy RDKQHLDDITAARLLPLHHLPAQLLSIEDSLALQKQQKQNYEEMQA

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_80 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_80 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000255529	1 retrocopy	retro_hsap_2941,
Sus scrofa	ENSSSCG00000030605	1 retrocopy	retro_sscr_547,
Ictidomys tridecemlineatus	ENSSTOG00000026874	1 retrocopy	retro_itri_80 ,