RetrogeneDB ID: retro_itri_1036

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393360.1:5051699..5052290(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CHMP2B
• Ensembl ID: ENSSTOG00000011456
• Aliases: None
• Description: charged multivesicular body protein 2B [Source:HGNC Symbol;Acc:24537]

Sequence

>retro_itri_1036
GATGTGATAAAGGAACAGATTTGAGAGTTACAGGGTACACAGAGGGCCATAACCAGAGATGTAGCAGCTGTAGAGAAACC
AGGAAAAATCTGTGATCAGAAGTTAAGAAAATGGCCAATACCGATAGTAAAGAAGCTCGCAGGGTTTTAGTTTAGTAGCT
TGTACCTTTGTGGAAACAGAAAACAAGAAATTCTGCTTTAAGTTAAAAAATGAACTCCTATGTCCATGCAAACCACAGTG
ATGCATTTCCAGAAGAAAATGGCTACAGCAACATCTATCACAGCAAAAGAAATATAGGCAGTTAGGAAAATGACAGATTC
ACATAGGACATTGCAATTAATGCACAACTTCTTGAAAGAAAGTATGAAAATGGAAATGAGTAAAGAAATGATCAGTGACA
CACTTGATGATGTCTTTGATGGTTCTAATGACGAAGAAGGAATCCAGTATATGGTGAATCAAGCTTCTGAAGAAATTGGA
ATAGAAGATTCTGGAAAGGTGGTCACAGTTCTCTCAGCTGCCTGAAGCTTACTATTTGCCTCTCCTTGAAAGGTTCAGTC
ATCAGTGAAGGCGCTGAATGACAAAACAAAG

Alignment

ORF - retro_itri_1036 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.78 %
• Parental protein coverage: 92.49 %
• Number of stop codons detected: 8
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DVIKEQNRELRGTQRAIIRDRAALEK-QEKQLELEIKKMAKIGNKEACRVLAKQLVHLRKQKTRTFAVSS
          DVIKEQ..EL.GTQRAI.RD.AA.EK...K.L..E.KKMA....KEA.RVL...LV.L.KQKTR..A.S.
Retrocopy DVIKEQI*ELQGTQRAITRDVAAVEK<TRKNL*SEVKKMANTDSKEARRVLV**LVPLWKQKTRNSALS*

Parental  KV-TSMSTQTKVMNSQMKMAGAMSTTAKTMQAVNKKMDPQKTLQTMQNFQKENMKMEMTEEMINDTLDDI
          K..T.MS.QT.VM..Q.KMA.A.S.TAK...AV.K..D...TLQ.M.NF.KE.MKMEM..EMI.DTLDD.
Retrocopy KM>TPMSMQTTVMHFQKKMATATSITAKEI*AVRKMTDSHRTLQLMHNFLKESMKMEMSKEMISDTLDDV

Parental  FDGSDEEEESQDIVNQVLDEIGIEISGKMAKAPSAARSLPSASTSKATISDEEIERQLK
          FDGS..EE..Q..VNQ...EIGIE.SGK.....SAA.SL..AS..K...S........K
Retrocopy FDGSNDEEGIQYMVNQASEEIGIEDSGKVVTVLSAA*SLLFASP*KVQSSVKALNDKTK

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_1036 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1036 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 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006615	2 retrocopies	retro_chof_2662, retro_chof_309,
Macropus eugenii	ENSMEUG00000012195	1 retrocopy	retro_meug_106,
Myotis lucifugus	ENSMLUG00000009052	1 retrocopy	retro_mluc_1557,
Monodelphis domestica	ENSMODG00000016939	2 retrocopies	retro_mdom_522, retro_mdom_605,
Ictidomys tridecemlineatus	ENSSTOG00000011456	1 retrocopy	retro_itri_1036 ,