RetrogeneDB ID: retro_itri_1271

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393420.1:2172629..2173143(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BRCC3
• Ensembl ID: ENSSTOG00000019781
• Aliases: None
• Description: BRCA1/BRCA2-containing complex, subunit 3 [Source:HGNC Symbol;Acc:24185]

Sequence

>retro_itri_1271
GCGGTTCATCTGGAGTCTGATGCTTTCCTAGTTTGTCTCAACCATGCTCTGAGAACAGAAAAGGAGGAGATGATGAGGCT
GTGTATAGGGGAGTTGAATGATGACACAGAGTGACTCCAAATTTGCATATACCAGAACAGAAATGTGCACAATTACTGAA
CAGGTTGACACCATCAGAATTGTTCATATTCATTCTGTCATCATCTTTCGGTGTTCTGATGAAAGGCAGGACAGAGTAGA
AATTTCTCCAGAGCAGCTTTCTGTGGCCTCAACAGAGACAGAGACGTTGGCTGAATTAACAGGTCACGCCAGGGGAGTTG
TGGACTGGTATCATTCCCATCCTCATATAACTGTTTGGCCTTCACATTTTGATGTTCGCACACAAGCCATGTACCAGGTG
ATGGATCAAAGTTTTGTAGTACTGATTTTTTCCTGTTTCACAGAGGATAAAAACACAAAGACTGTGTAGGTACTCAACAC
TTGCTTCTAAGCCATACAGGCCCCAAAAAGCTCA

Alignment

ORF - retro_itri_1271 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.71 %
• Parental protein coverage: 94.51 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AVHLESDAFLVCLNHALSTEKEEVMGLCIGEVSSP-HR-SDSKFAYTGTEMRTVAEKVDTVRIVHIHSVI
          AVHLESDAFLVCLNHAL.TEKEE.M.LCIGE.....HR.SDSKFAYT.TEM.T..E.VDT.RIVHIHSVI
Retrocopy AVHLESDAFLVCLNHALRTEKEEMMRLCIGELNDD<HR<SDSKFAYTRTEMCTITEQVDTIRIVHIHSVI

Parental  ILRRSDKRKDRVEISPEQLSAASTEAELIDLKESLGLLVVGWYHSHPHITVWPSHVDVRTQAMYQMMDQG
          I.R.SD.R.DRVEISPEQLS.ASTE.E...........VV.WYHSHPHITVWPSH.DVRTQAMYQ.MDQ.
Retrocopy IFRCSDERQDRVEISPEQLSVASTETETLAELTGHARGVVDWYHSHPHITVWPSHFDVRTQAMYQVMDQS

Parental  FVGLIFSCFIEDKNTKTGRVLYTCFQSIQAQKSS
          FV.LIFSCF.EDKNTKT..VL.TCF..IQA.KSS
Retrocopy FVVLIFSCFTEDKNTKTV*VLNTCF*AIQAPKSS

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_1271 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1271 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 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007817	2 retrocopies	retro_btau_1327, retro_btau_1646,
Cavia porcellus	ENSCPOG00000001882	2 retrocopies	retro_cpor_388, retro_cpor_627,
Monodelphis domestica	ENSMODG00000016487	1 retrocopy	retro_mdom_930,
Mus musculus	ENSMUSG00000031201	1 retrocopy	retro_mmus_672,
Sarcophilus harrisii	ENSSHAG00000005392	1 retrocopy	retro_shar_51,
Ictidomys tridecemlineatus	ENSSTOG00000019781	2 retrocopies	retro_itri_1271 , retro_itri_806,