RetrogeneDB ID: retro_itri_286

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393282.1:21201189..21201885(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: STARD3NL
• Ensembl ID: ENSSTOG00000014750
• Aliases: None
• Description: STARD3 N-terminal like [Source:HGNC Symbol;Acc:19169]

Sequence

>retro_itri_286
TTGACCCACCTGCCAGACGACAAGGAGAATATGCTCACTGGGAGCCAGAGCTCACATGCTTCTCTGAGCAATGTCCACTC
CATCAACCTCATGCAACTTATGGCCAGTATGGAGTCCTATGAAGGAAGGGAAAAGAAAGGCATATCCGATGTCAGGAGGA
CTTTCTGTTTGTTTATCACCTTTGACCTCTTATTTGTAACACTGTTGTGGATAATAGGGTTAAATGTGAACAGAGCTATT
GAAAACACGTTAGAGAAGGTGATACAGATGACTACTCCTCATCTTATTTTGGTACATTTCTTTTGGCAGTTTTTCAATAT
AAAGTGTTGATACTCGCCTAGGCTGCATGCAGACTGTGCCACTGGTGGGCAGTAGCGTTGACAACAGCAGTGACCAGTGC
CTTTTTAATAGCAAAAGTGATCCTTTCAAAGCTTTCCTCCCTAAGGAGCTTTTGGCTATGTGCTGCCCAGCATTTCATTC
ATTCTCGCCTGGATCCAGACATAGTTCATGGATTTCAAAGTGTTACCTTGAGAAGCAGCAGAAGAAAGGAGACTCCTGAT
AGTTCAGGATGCCTCAGAGAGGGCATTCCTCATATCAGCTGGTCTTTCTGATGGTCAGTTTTATTCCTCTTCTAAAGATG
AGGTAGGATCTGAAGAAGCTGAGGAAAAACAGGAATGTGAAAAACCTCTTTTAGAA

Alignment

ORF - retro_itri_286 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.24 %
• Parental protein coverage: 99.57 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MNHLPD-MENTLTGSQSSHASLREVHSINPTQLMARIESYEGREKKGISDVRRTFCLFVTFDLLFVTLLW
          ..HLPD..EN.LTGSQSSHASL..VHSIN..QLMA..ESYEGREKKGISDVRRTFCLF.TFDLLFVTLLW
Retrocopy LTHLPDDKENMLTGSQSSHASLSNVHSINLMQLMASMESYEGREKKGISDVRRTFCLFITFDLLFVTLLW

Parental  IIELNVNGGIENTLEKEVVQY-DYYSSYFDIFLLAVFRFKVLILAYAVCRLRHWWAIALTTAVTSAFLLA
          II.LNVN..IENTLEK.V.Q..DY.SSYF..FLLAVF..KVLILA.A.CRL.HWWA.ALTTAVTSAFL.A
Retrocopy IIGLNVNRAIENTLEK-VIQM<DYSSSYFGTFLLAVFQYKVLILA*AACRLCHWWAVALTTAVTSAFLIA

Parental  KVILSKLFSQ-GAFGYVLPIISFILAWIETWFLDFKVLPQEAEEENRLLIVQDASERAALIPAGLSDGQF
          KVILSKL.S..GAFGYVLP.ISFILAWI.T.F.DFKVLP.EA.EE.RLLIVQDASERA.LI.AGLSDGQF
Retrocopy KVILSKLSSL>GAFGYVLPSISFILAWIQT*FMDFKVLP*EAAEERRLLIVQDASERAFLISAGLSDGQF

Parental  YSPPESEAGSEEEAEEKQDSEKPLLE
          YS....E.GS.EEAEEKQ..EKPLLE
Retrocopy YSSSKDEVGS-EEAEEKQECEKPLLE

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_286 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_286 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 10 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000038795	1 retrocopy	retro_btau_264,
Choloepus hoffmanni	ENSCHOG00000008990	1 retrocopy	retro_chof_984,
Callithrix jacchus	ENSCJAG00000012622	1 retrocopy	retro_cjac_3042,
Cavia porcellus	ENSCPOG00000004394	1 retrocopy	retro_cpor_1237,
Dasypus novemcinctus	ENSDNOG00000017960	1 retrocopy	retro_dnov_2389,
Equus caballus	ENSECAG00000005250	1 retrocopy	retro_ecab_709,
Microcebus murinus	ENSMICG00000000945	1 retrocopy	retro_mmur_388,
Macaca mulatta	ENSMMUG00000023659	1 retrocopy	retro_mmul_2643,
Ictidomys tridecemlineatus	ENSSTOG00000014750	1 retrocopy	retro_itri_286 ,
Tursiops truncatus	ENSTTRG00000004099	1 retrocopy	retro_ttru_864,