RetrogeneDB ID: retro_itri_316

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393284.1:2125939..2126666(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000023902
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NSDHL
• Ensembl ID: ENSSTOG00000019379
• Aliases: None
• Description: NAD(P) dependent steroid dehydrogenase-like [Source:HGNC Symbol;Acc:13398]

Sequence

>retro_itri_316
ATAGAAGAAGCAGTTGGTGAGCCAGTGAGAGAGCAGGACACGTGGATCCAGGTGATAGAGGACATTCCCAAGGTCAAGAA
CTGCACAGGGATCGGAGGCTCTGGATTCCTGGGGCAGCACATGGTGGAGCCGTTGCTTGCAAGGGGCTACACCGCCAACG
TATTCGATATCCGGCAAGGTTTTGATAATCCCCGGGTGCAGTTCTTTCTGGGTGACCTCTGCAACCGAGAGGACCTGCAC
CCAGCTCTGAGAGGTGTGAGCGCAGTTTTCCACTGTGCATCACCCCCACCCTCCAGTAACGACAAGGAGCTCCTTTCTAG
AGTGAATTTCACTGGCACCAAGGATGTCATTGAAACTTGCACAGAGGCTGGAGTCCAGAAACTCGTTTTGACCGGCAGTG
CCAGTGTCATCTTTGAGGGCAGTGACGTCAAAAATGGAACCGAAGACCTTCCTTATGCCACGAAACCCATCGACTACTTA
CACGGAGACCAAAGTCCTACAAGAGAAAGCAGTTCTGGACGCCAGTGATCCTGAGAGAGGTTTCTTAACCCCAGCTATCC
GTCCTCATGGCGTTTTTGGCCTAGGAGATCCCCAGTTGGTCCCCATCCTCACTGAGGCAGCCGAGAAGGACAAGATGAAG
TTCACGATGGGGAACGGGAAGAACCAGCAAGATGATGATGACGGTAGATCTCACCTCCGTGGAGAAGTGGTCATCCATGG
ACACATC

Alignment

ORF - retro_itri_316 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.95 %
• Parental protein coverage: 67.04 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MEQAVGEAVREQVTRTHVIEDIPKVKNCTVIGGSGFLGQHMVEQLLARGYTVNVFDIRQGFDNPRVQFFL
          .E.AVGE.VREQ.T...VIEDIPKVKNCT.IGGSGFLGQHMVE.LLARGYT.NVFDIRQGFDNPRVQFFL
Retrocopy IEEAVGEPVREQDTWIQVIEDIPKVKNCTGIGGSGFLGQHMVEPLLARGYTANVFDIRQGFDNPRVQFFL

Parental  GDLCNQEDLYPALKGVSTVFHCASPPPSSNNKELFYRVNFIGTKNVIETCKKAGVQKLILTSSASVIFEG
          GDLCN.EDL.PAL.GVS.VFHCASPPPSSN.KEL..RVNF.GTK.VIETC..AGVQKL.LT.SASVIFEG
Retrocopy GDLCNREDLHPALRGVSAVFHCASPPPSSNDKELLSRVNFTGTKDVIETCTEAGVQKLVLTGSASVIFEG

Parental  SDIKNGTEDLPYAMKPIDY-YTETKILQERAVLDANDPERNFLTTAIRPHGIFGPGDPQLVPILIEAAKK
          SD.KNGTEDLPYA.KPIDY.YTETK.LQE.AVLDA.DPER.FLT.AIRPHG.FG.GDPQLVPIL.EAA.K
Retrocopy SDVKNGTEDLPYATKPIDY>YTETKVLQEKAVLDASDPERGFLTPAIRPHGVFGLGDPQLVPILTEAAEK

Parental  GKMKFMIGNGKNLVDFTFVENVVHGHILAAEHL
          .KMKF..GNGKN..D.........G......H.
Retrocopy DKMKFTMGNGKNQQDDDDGRSHLRGEVVIHGHI

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_316 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_316 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryctolagus cuniculus	ENSOCUG00000007899	1 retrocopy	retro_ocun_602,
Ictidomys tridecemlineatus	ENSSTOG00000019379	1 retrocopy	retro_itri_316 ,