RetrogeneDB ID: retro_itri_460

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393293.1:14544764..14545864(+)
• Located in intron of: ENSSTOG00000021107

Retrocopy information

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

Parental gene information

• Parental gene symbol: DRG1
• Ensembl ID: ENSSTOG00000014187
• Aliases: None
• Description: developmentally regulated GTP binding protein 1 [Source:HGNC Symbol;Acc:3029]

Sequence

>retro_itri_460
ATGAGTAGCACTTTAGCAAAGATCGCAGAGATCAAAGCCGAGATGGCTCGGACTCAAAAGAACAAGGCAACAGCACACCA
CCTAGGGCTGCTTAAGGCTCGCCTTGCTAAGCTTCGTAGAGAACTCATTACTCCAAAAGGTGGTAGAGGTGGTGGGCCAG
GAGAAGGTTTTGATGTGGCCAACACTGGTGATCTCGAATTAAGTCTGTGGGTTTTCCATCTGTGGGGAAGTCAACACTAC
TGAGTAACTTGGCTGGGGTATATTCTGAAATGGCAGCCTATGAATTTACTACCCTAACTACTGTGCCTGGTGTCATCACA
TACAAAGGTGCCAAAAAACAGCTTCTGGAACTCCCAGGTATCATTGAAGGTGCCAAGGATGGGAAAGGTAGGGGCTGTCA
GGTTATTGCAGTGACCTGAGCATGCAATTTGATCCTGATTGTTCTGGAAGTCCTGAAGCCACTAGGACATAAGAAGGTAA
CTGAAAATGAATTGGAAGGCTTTGGTATTTGCTTGAATAGTAAACCTCCCAACATTGGCTTTAAGAAGAAAGATAAAGGA
GGCATTAATCTCACAACTACCTGCCCTCAGAGTGAGCTGGATGCTGAAACTGTGAAGAGCATTCTTGCTAAATACAAAAT
TCATAATGCTGATGTGACTTTGCGTAGTAATGCCACAGCTGATGACTTCATTGATGTGGTGGAAGGAAACAGGGTTTATA
TTCCTTGTATTTATGTATTAAATAAAATCGATCAAATCTCCATTGAGGAATTGGATATCATCTATAAAGTGCCTCACTGT
GTACCCATCTCTGCCCATCACCGCTGGAATTTTGATGACCTGTTAGAAAAGATCTGGGACTATTTGAAACTAGTGAGAAT
TTACACCAAACCCAAAGGCCAGTTACCAGATTACACATCTCCAGTGGTGCTGCCTTACTCCAGGACCACGGTGAAGGATT
TCTGCATGAAGATCCACAAAAATCTTATCAAAGAATTTAAATACGCTCTGGTCTGGGGTCTCTCTGTGAAACACAATCCA
CAGAAAGTGGGTAACGACCATACATTGGAGGACGAGGATGTCATTCAGATTGTGAAGAAA

Alignment

ORF - retro_itri_460 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.22 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSSTLAKIAEIEAEMARTQKNKATAHHLGLLKARLAKLRRELITPKGGGGGGPGEGFDVAKTGD-ARIGF
          MSSTLAKIAEI.AEMARTQKNKATAHHLGLLKARLAKL............GGPGEGFDVA.TGD..RI..
Retrocopy MSSTLAKIAEIKAEMARTQKNKATAHHLGLLKARLAKLXXXXXXXXXXXXGGPGEGFDVANTGD<SRIKS

Parental  VGFPSVGKSTLLSNLAGVYSEVAAYEFTTLTTVPGVIRYKGAKIQLLDLPGIIEGAKDGKGRGRQVIAVA
          VGFPSVGKSTLLSNLAGVYSE.AAYEFTTLTTVPGVI.YKGAK.QLL.LPGIIEGAKDGKGRG.QVIAV.
Retrocopy VGFPSVGKSTLLSNLAGVYSEMAAYEFTTLTTVPGVITYKGAKKQLLELPGIIEGAKDGKGRGCQVIAVT

Parental  RTCNLILIVLDVLKPLGHKKIIENELEGFGIRLNSKPPNIGFKKKDKGGINLTATCPQSELDAETVKSIL
          ..CNLILIVL.VLKPLGHKK..ENELEGFGI.LNSKPPNIGFKKKDKGGINLT.TCPQSELDAETVKSIL
Retrocopy *ACNLILIVLEVLKPLGHKKVTENELEGFGICLNSKPPNIGFKKKDKGGINLTTTCPQSELDAETVKSIL

Parental  AEYKIHNADVTLRSDATADDLIDVVEGNRVYIPCIYVLNKIDQISIEELDIIYKVPHCVPISAHHRWNFD
          A.YKIHNADVTLRS.ATADD.IDVVEGNRVYIPCIYVLNKIDQISIEELDIIYKVPHCVPISAHHRWNFD
Retrocopy AKYKIHNADVTLRSNATADDFIDVVEGNRVYIPCIYVLNKIDQISIEELDIIYKVPHCVPISAHHRWNFD

Parental  DLLEKIWDYLKLVRIYTKPKGQLPDYTSPVVLPYSRTTVEDFCMKIHKNLIKEFKYALVWGLSVKHNPQK
          DLLEKIWDYLKLVRIYTKPKGQLPDYTSPVVLPYSRTTV.DFCMKIHKNLIKEFKYALVWGLSVKHNPQK
Retrocopy DLLEKIWDYLKLVRIYTKPKGQLPDYTSPVVLPYSRTTVKDFCMKIHKNLIKEFKYALVWGLSVKHNPQK

Parental  VGKDHTLEDEDVIQIVKK
          VG.DHTLEDEDVIQIVKK
Retrocopy VGNDHTLEDEDVIQIVKK

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_460 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_460 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 17 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007040	1 retrocopy	retro_amel_1448,
Canis familiaris	ENSCAFG00000032601	6 retrocopies	retro_cfam_1535, retro_cfam_1807, retro_cfam_382, retro_cfam_415, retro_cfam_453, retro_cfam_607,
Ciona intestinalis	ENSCING00000003305	1 retrocopy	retro_cint_1,
Callithrix jacchus	ENSCJAG00000011009	4 retrocopies	retro_cjac_1104, retro_cjac_2246, retro_cjac_2606, retro_cjac_855,
Cavia porcellus	ENSCPOG00000010791	1 retrocopy	retro_cpor_1401,
Ciona savignyi	ENSCSAVG00000006503	1 retrocopy	retro_csav_10,
Dasypus novemcinctus	ENSDNOG00000001312	1 retrocopy	retro_dnov_531,
Homo sapiens	ENSG00000185721	1 retrocopy	retro_hsap_2231,
Gorilla gorilla	ENSGGOG00000011185	1 retrocopy	retro_ggor_1665,
Myotis lucifugus	ENSMLUG00000007033	1 retrocopy	retro_mluc_1447,
Macaca mulatta	ENSMMUG00000019099	1 retrocopy	retro_mmul_999,
Mustela putorius furo	ENSMPUG00000012810	1 retrocopy	retro_mputfur_339,
Mus musculus	ENSMUSG00000020457	1 retrocopy	retro_mmus_2366,
Nomascus leucogenys	ENSNLEG00000027001	1 retrocopy	retro_nleu_2627,
Pan troglodytes	ENSPTRG00000014272	1 retrocopy	retro_ptro_1578,
Ictidomys tridecemlineatus	ENSSTOG00000014187	1 retrocopy	retro_itri_460 ,
Tarsius syrichta	ENSTSYG00000010160	3 retrocopies	retro_tsyr_1374, retro_tsyr_1918, retro_tsyr_405,