RetrogeneDB ID: retro_itri_50

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393305.1:5391321..5392380(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000000288
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: TMEM30A
• Ensembl ID: ENSSTOG00000002543
• Aliases: None
• Description: transmembrane protein 30A [Source:HGNC Symbol;Acc:16667]

Sequence

>retro_itri_50
ATGACCTGGAGCGCCACGGCCCGGGGCGCCCACCAGCCGGACAACACCGCGTTCACGCAGCAGCGCCTCCCCGCCTGGCA
GCCGCTGCTGTCCGCCAGCATCACGCTACCGCTCTTCTTTTGCGCGGGCCTGGCCTTCATCGGCCTGGGCCTGGGCCTCT
ACTACTCTTCCAACGGCATCAAGGAGCTCGAGTACGACTACACTGGCGACCCAGGCACCGGCAACTGCTCTGTGTGCGCA
GCCGAAGGCCAGGGCCGCGCGCCGCCGCCTAATTGCTCGTGCGCCTGGTACTTCTCGCTGCCCGAGCTCTTCCCGGGCCC
CGTCTACCTCTACTACGAGCTGACCAACTTCTACCAGAACAACCGCCGCTATGGCGTGTCCCGCGACGACGCGCAGCTGA
GCGGGCTGCCGAGCGCGTTGCACAACCCGGTCAACGAGTGCGCCCCCTACCAGTTCAGCGCGACCGGCCTGCCCATCGCG
CCCTGCGGCGCCATCGCCAACAGCCTCTTCAATGACTCCTTCTCGCTGTGGCACCAGCGCCGGCCAGGCGGGCCCTACGT
CGAGGTGCCACTCGATCGCGCCGCCATCGCCTGGTGGACCGACTACCACGTCAAGTTCCACAACCCGCCGCTGGTGAATG
GCAGCCTGGCGCTGGCCTTTCGCGGCACGGCGCCCCCGCCCAACTGGCACCGGCCGGTGTACGAGCTCAGCCCCGACCCC
AACAACACCGGCTTCATCAACCAGGACTTCGTGGTGTGGATGCGCACCGCGGCGCTGCCCACGTTCCGCAAGCTGTTCGC
GCGCATCCGCCAGGGCAACTACACCGCAGGGCTGCCCCGGGGCGCCTACCGCGTCAACATCACTTACAACTACCCGGTGC
GCGTCTTCGGTGGCCACAAGCTCATCATCTTCAGCAATATCTCGTGGATGGGTGGCAAGAATCCTTTCCTGGGTATCGCC
TATCTGGTGGTCGGCTCCCTCTGCATCCTCATGGGTTTTGTCATGCTGGTGGTCTACATTCGCTATCAGGACCAGAATGA
GGAGGAGGACGACGACGAG

Alignment

ORF - retro_itri_50 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.2 %
• Parental protein coverage: 74.71 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  CICTINFTLEKSFEGNVFMYYGLSNFYQNHRRYVKSRDDSQLNGDRSALLNPSKECEPYRRNEDK-PIAP
          C.C...F.L...F.G.V..YY.L.NFYQN.RRY..SRDD.QL.G..SAL.NP..EC.PY.......PIAP
Retrocopy CSCAWYFSLPELFPGPVYLYYELTNFYQNNRRYGVSRDDAQLSGLPSALHNPVNECAPYQFSATGLPIAP

Parental  CGAIANSMFNDTLELFLVANESDPTLMLIPLKRRGIAWWTDKNVKFRNPPGTE-SLKERFKDTTHPVNWL
          CGAIANS.FND...L........P.....PL.R..IAWWTD..VKF.NPP....SL...F..T..P.NW.
Retrocopy CGAIANSLFNDSFSLWHQRRPGGPYVE-VPLDRAAIAWWTDYHVKFHNPPLVNGSLALAFRGTAPPPNWH

Parental  KPVYELDPEDEDNNGFINEDFIVWMRTAALPTFRKLYRLIERKNDLHPTLPAGRYYLNITYNYPVHSFDG
          .PVYEL.P.D..N.GFIN.DF.VWMRTAALPTFRKL...I.R.......LP.G.Y..NITYNYPV..F.G
Retrocopy RPVYELSP-DPNNTGFINQDFVVWMRTAALPTFRKLFARI-RQGNYTAGLPRGAYRVNITYNYPVRVFGG

Parental  RKRMILSTVSWMGGKNPFLGIAYITIGSISFLLGVVLLVINHKYRNSSNTAD
          .K..I.S..SWMGGKNPFLGIAY...GS...L.G.V.LV....Y.......D
Retrocopy HKLIIFSNISWMGGKNPFLGIAYLVVGSLCILMGFVMLVVYIRYQDQNEEED

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_50 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_50 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 15 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005100	1 retrocopy	retro_btau_72,
Canis familiaris	ENSCAFG00000002708	1 retrocopy	retro_cfam_26,
Callithrix jacchus	ENSCJAG00000010325	1 retrocopy	retro_cjac_801,
Cavia porcellus	ENSCPOG00000020712	1 retrocopy	retro_cpor_23,
Homo sapiens	ENSG00000112697	1 retrocopy	retro_hsap_12,
Myotis lucifugus	ENSMLUG00000011923	1 retrocopy	retro_mluc_1871,
Monodelphis domestica	ENSMODG00000018502	1 retrocopy	retro_mdom_287,
Mus musculus	ENSMUSG00000032328	1 retrocopy	retro_mmus_108,
Nomascus leucogenys	ENSNLEG00000004962	1 retrocopy	retro_nleu_69,
Otolemur garnettii	ENSOGAG00000015718	1 retrocopy	retro_ogar_22,
Pongo abelii	ENSPPYG00000016782	1 retrocopy	retro_pabe_204,
Pelodiscus sinensis	ENSPSIG00000007174	1 retrocopy	retro_psin_61,
Rattus norvegicus	ENSRNOG00000010895	1 retrocopy	retro_rnor_399,
Ictidomys tridecemlineatus	ENSSTOG00000002543	1 retrocopy	retro_itri_50 ,
Tarsius syrichta	ENSTSYG00000008211	1 retrocopy	retro_tsyr_928,