RetrogeneDB ID: retro_itri_262

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393281.1:7677850..7678338(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM168B
• Ensembl ID: ENSSTOG00000000206
• Aliases: None
• Description: family with sequence similarity 168, member B [Source:HGNC Symbol;Acc:27016]

Sequence

>retro_itri_262
GTTTATCCAAATGGTTTCCCCATGGGCTATGCAGCTGCAGCCCCTGCCTATTCTCTACCTTGGAGGGAATCCTACCTTCC
AAACAGGTTACACTCCTGGCACACCTTACAAAGTGTCCTGTCCCCCAACAGCTGGGCCGTGCCACCATACTCTTCTTCTT
CTGACCCTGTGGGAAGTCCCCACCCCCAGCAGAACCCTTGCACAGCAAGGCATGTACTACACACAGCCACTTATGCAACA
CCTACTCACGTCATCCTTCACACCCTGGTGGTGCAGCCCAATGGAATGCAGCTATAGTGTACCCTGATCCCATCCCTCCT
CCTAGAGGCAATGGGGTCATATGGGCATGGTTCCTGGGATCATGATGACCATGTCAGCAGGTACCCTGCTGACTGTTCAC
TTCCCAACTCCTGTTGCTCCTCGCCCAGTCACTGCCCACATACCAGGTCCCAGGAATACCCACCTACAGCTATATGCCCC
GTCAGTGG

Alignment

ORF - retro_itri_262 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.72 %
• Parental protein coverage: 80.68 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  MYPGANPTFQTVLDIARGLLNLDCYTPGTPYKVSCSPTSGAVPPYSSSPNPYQTAVYPVRSAY-PQQSPY
          .YP...P........A..L.....Y.P......S.........P.S....PY.....PV.S...P...P.
Retrocopy VYPNGFPMGYAAAAPAYSLPWRESYLPNRLH--SWHTLQSVLSPNSWAVPPYSSSSDPVGSPH<PPAEPL

Parental  -AQQGTYYTQPL-YAAPPHVIHHTTVVQPNGMP-ATVYPAPIPPPRGNGVT-MGMVAGTTMAMSAGTLLT
          .AQQG.YYTQPL.YA.P.HVI.HT.VVQPNGM..A.VYP.PIPPPRGNGV..MGMV.G..M.MSAGTLLT
Retrocopy <AQQGMYYTQPL<YATPTHVILHTLVVQPNGMQ<AIVYPDPIPPPRGNGVI<MGMVPGIMMTMSAGTLLT

Parental  AHSPTPVAPHPVTV-PTYRAPGTP-TYSYVPPQW
          .H.PTPVAP.PVT..P..R....P.TYSY.P.QW
Retrocopy VHFPTPVAPRPVTA<PHTRSQEYP<TYSYMPRQW

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_262 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_262 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 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000004222	2 retrocopies	retro_cfam_1748, retro_cfam_344,
Choloepus hoffmanni	ENSCHOG00000009590	1 retrocopy	retro_chof_551,
Equus caballus	ENSECAG00000017018	1 retrocopy	retro_ecab_27,
Felis catus	ENSFCAG00000000303	1 retrocopy	retro_fcat_1218,
Monodelphis domestica	ENSMODG00000018633	1 retrocopy	retro_mdom_1625,
Mustela putorius furo	ENSMPUG00000011824	1 retrocopy	retro_mputfur_454,
Ictidomys tridecemlineatus	ENSSTOG00000000206	2 retrocopies	retro_itri_191, retro_itri_262 ,
Ictidomys tridecemlineatus	ENSSTOG00000014507	1 retrocopy	retro_itri_1722,
Tupaia belangeri	ENSTBEG00000017162	1 retrocopy	retro_tbel_83,