RetrogeneDB ID: retro_itri_8

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393279.1:50303975..50305028(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000020073
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: TMEM185A
• Ensembl ID: ENSSTOG00000014484
• Aliases: None
• Description: transmembrane protein 185A [Source:HGNC Symbol;Acc:17125]

Sequence

>retro_itri_8
ATGAACCCCAGGGGCCTGTTCCAGGACTTCAACCCGAGTAAGTTCCTAATCTACGCCTGCCTGCTGCTCTTCTCCGTGCT
GCTGCCCCTCCGTCTGGACGGCATCATCCAGTGGAGCTACTGGGCCGTCTTCGCCCCCATATGGCTGTGGAAGCTCCTGG
TCATCTCGGGCGCCTCGGTGGGCGCTGGCGTTTGGGCCCGCAACCCTCGCTACCGCACCGAGGGGGAGGCCTGCGTAGAG
TTCAAAGCCATGCTGATCGCCGTAGGCATCCACCTGCTGCTGCTCATGTTCGAAGTCCTAGTCTGTGACCGTGTGGAGAG
AGGGACTCACTTCTGGCTGCTGGTCTTCATGCCACTCTTCTTCGTCTCCCCGGTGTCTGTGGCCGCCTGCGTCTGGGGCT
TCCGACACGATAGGTCGCTGGAGCTGGAGATCTTGTGCTCAGTCAACATCCTGCAGTTCATCTTTATTGCCTTGAGGCTG
GACAGGATTATCCACTGGCCGTGGCTGGTGGTGTTCGTCCCCCTGTGGATCCTCATGTCATTTCTTTGCCTGGTCGTCCT
GTATTACATCGTGTGGTCCCTTCTGTTCCTGCGATCCCTGGATGTGGTAGCTGAACAGCGAAGAACTCATGTCACCATGG
CCATCAGCTGGATAACAATTGTGGTGCCTCTGCTCACTTTTGAGGTCCTACTGGTTCACAGATTGGATGGGCACAACACA
TTCTCTTACATCTCCATCTTTATCCCCCTTTGGCTCTCATTAATAACTTTGATGGCTACAACGTTTAGGCGAAAAGGAGG
CAATCATTGGTGGTTTGGTATTCGCAGAGATTTCTGTCAGTTTCTGCTTGAAATTTTCCCATTTTTAAGAGAATATGGGA
ACATTTCATATGATCTCCATCATGAAGATAGCGAAGATGCTGAGGAAACATCCGGTCCAGAAGCTCCAAAAATTGCTCCA
ATGTTTGGAAAGAAGGCCAGGGTGGTTATAACACAGAGCCCTGGAAAATATGTTCCTCCACCCCCCAAGTTAAATATTGA
TATGCCAGACTAA

Alignment

ORF - retro_itri_8 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.13 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  INIKKIFFYFSPSKFLIYACLLLFSVLLALRLDGIIQWSYWAVFAPIWLWKLMVIVGASVGTGVWARNPQ
          .N....F..F.PSKFLIYACLLLFSVLL.LRLDGIIQWSYWAVFAPIWLWKL.VI.GASVG.GVWARNP.
Retrocopy MNPRGLFQDFNPSKFLIYACLLLFSVLLPLRLDGIIQWSYWAVFAPIWLWKLLVISGASVGAGVWARNPR

Parental  YRAEGETCVEFKAMLIAVGIHLLLLMFEVLVCDRIERGSHFWLLVFMPLFFVSPVSVAACVWGFRHDRSL
          YR.EGE.CVEFKAMLIAVGIHLLLLMFEVLVCDR.ERG.HFWLLVFMPLFFVSPVSVAACVWGFRHDRSL
Retrocopy YRTEGEACVEFKAMLIAVGIHLLLLMFEVLVCDRVERGTHFWLLVFMPLFFVSPVSVAACVWGFRHDRSL

Parental  ELEILCSVNILQFIFIALRLDKIIHWPWLVVCVPLWILMSFLCLVVLYYIVWSVLFLRSMDVIAEQRRTH
          ELEILCSVNILQFIFIALRLD.IIHWPWLVV.VPLWILMSFLCLVVLYYIVWS.LFLRS.DV.AEQRRTH
Retrocopy ELEILCSVNILQFIFIALRLDRIIHWPWLVVFVPLWILMSFLCLVVLYYIVWSLLFLRSLDVVAEQRRTH

Parental  ITMALSWMTIVVPLLTFEILLVHKLDGHNAFSCIPIFVPLWLSLITLMATTFGQKGGNHCTYSV
          .TMA.SW.TIVVPLLTFE.LLVH.LDGHN.FS.I.IF.PLWLSLITLMATTF..KGGNH.....
Retrocopy VTMAISWITIVVPLLTFEVLLVHRLDGHNTFSYISIFIPLWLSLITLMATTFRRKGGNHWWFGI

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_8 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_8 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 22 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000008637	1 retrocopy	retro_acar_65,
Ailuropoda melanoleuca	ENSAMEG00000009351	1 retrocopy	retro_amel_8,
Cavia porcellus	ENSCPOG00000003622	1 retrocopy	retro_cpor_5,
Dasypus novemcinctus	ENSDNOG00000011864	1 retrocopy	retro_dnov_2451,
Dipodomys ordii	ENSDORG00000015027	1 retrocopy	retro_dord_67,
Equus caballus	ENSECAG00000009399	1 retrocopy	retro_ecab_426,
Homo sapiens	ENSG00000155984	1 retrocopy	retro_hsap_104,
Gorilla gorilla	ENSGGOG00000024268	1 retrocopy	retro_ggor_189,
Loxodonta africana	ENSLAFG00000003044	1 retrocopy	retro_lafr_898,
Microcebus murinus	ENSMICG00000004639	1 retrocopy	retro_mmur_106,
Myotis lucifugus	ENSMLUG00000001319	1 retrocopy	retro_mluc_2075,
Macaca mulatta	ENSMMUG00000002888	1 retrocopy	retro_mmul_310,
Mustela putorius furo	ENSMPUG00000011896	1 retrocopy	retro_mputfur_46,
Mus musculus	ENSMUSG00000073139	1 retrocopy	retro_mmus_358,
Nomascus leucogenys	ENSNLEG00000013487	1 retrocopy	retro_nleu_2723,
Otolemur garnettii	ENSOGAG00000016414	1 retrocopy	retro_ogar_88,
Pongo abelii	ENSPPYG00000020809	1 retrocopy	retro_pabe_118,
Pteropus vampyrus	ENSPVAG00000013822	1 retrocopy	retro_pvam_30,
Rattus norvegicus	ENSRNOG00000011047	1 retrocopy	retro_rnor_6,
Sus scrofa	ENSSSCG00000012739	1 retrocopy	retro_sscr_494,
Ictidomys tridecemlineatus	ENSSTOG00000014484	1 retrocopy	retro_itri_8 ,
Tursiops truncatus	ENSTTRG00000000643	1 retrocopy	retro_ttru_868,