RetrogeneDB ID: retro_itri_1696

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393641.1:977618..978334(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MAT2B
• Ensembl ID: ENSSTOG00000009459
• Aliases: None
• Description: methionine adenosyltransferase II, beta [Source:HGNC Symbol;Acc:6905]

Sequence

>retro_itri_1696
CACATTGTGCAGCAGAGAAGACCAGATGTTGTAGAGAATCAGCCAGATGCTGCTTCTCAATTTAATGTGGATGCTTCTGG
GAATTTAGCTAAGGAAGCAGCTGCAATTGGAGCATTTCTCATTTATATTAGCTCAGATTATCTATTTGATGGAAGGGATC
CACATTACAGTGAGGAAGACATACCAAGTCCCCTAAATTTGTAAGGTAAAACAAAATTAGGAGAAAAGGCAGTCCTGAAG
AATAACTTGGAAGCTGCCGTTTTGAGAATTCCTGTTCTGTATGGAGAAGTTGAAAAGCTTGAAGAAAGCGCTGTGACGGT
CATGTTTGACAAAGTGCAGTTCAGCAACAAGTCAGCAAACATGGACCACTGGCATCAGAGGTTTCCCACACATGTCAAAG
ATGTGGCTACAGTGTGTTGGCAGCTGGCAGAGAAGAGAATGCTGTACCCATTAATTAAGGGAACCTTTCATTGGTCTGGT
AATGAACCGATGACCAAGTATGAAATGGCATGTGCATTGAAGATGCCTTCAACTTCCCCAGGAGTCACTTAAGACCTATC
ACTGACAGCCCAGTCATAGGAGCACAATGTCCACATAATGCTCAGCTTGACTGCTCCAAATTGGAGACCTTGGGCATTGG
CCAGCTAACACCATTTCAAATTGGAATCAAGGAATCACTCTGGCCTTTCCTCATTGACAAGAGAAGGAGACAGTCT

Alignment

ORF - retro_itri_1696 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.21 %
• Parental protein coverage: 71.86 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  HCAAERRPDVVENQPDAASQLNVDASGNLAKEAAAIGAFLIYISSDYVFDGTDPPYSEEDIPSPLNLYGK
          H....RRPDVVENQPDAASQ.NVDASGNLAKEAAAIGAFLIYISSDY.FDG.DP.YSEEDIPSPLNL.GK
Retrocopy HIVQQRRPDVVENQPDAASQFNVDASGNLAKEAAAIGAFLIYISSDYLFDGRDPHYSEEDIPSPLNL*GK

Parental  TKLEGEKAVLENNLGAAVLRIPVLYGEVEKLEESAVTVMFDKVQFSNKSANMDHWQQRFPTHVKDVATVC
          TKL.GEKAVL.NNL.AAVLRIPVLYGEVEKLEESAVTVMFDKVQFSNKSANMDHW.QRFPTHVKDVATVC
Retrocopy TKL-GEKAVLKNNLEAAVLRIPVLYGEVEKLEESAVTVMFDKVQFSNKSANMDHWHQRFPTHVKDVATVC

Parental  RQLAEKRMLDPSIKGTFHWSGNEQMTKYEMACA-IADAFNLPSSHLRPITDSPVIGAQRPHNAQLDCSKL
          .QLAEKRML.P.IKGTFHWSGNE.MTKYEMACA.I.DAFN.P.SHLRPITDSPVIGAQ.PHNAQLDCSKL
Retrocopy WQLAEKRMLYPLIKGTFHWSGNEPMTKYEMACA<IEDAFNFPRSHLRPITDSPVIGAQCPHNAQLDCSKL

Parental  ETLGIGQRTPFRIGIKESLWPFLIDKRWRQT
          ETLGIGQ.TPF.IGIKESLWPFLIDKR.RQ.
Retrocopy ETLGIGQLTPFQIGIKESLWPFLIDKRRRQS

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_1696 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1696 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 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012350	1 retrocopy	retro_btau_387,
Callithrix jacchus	ENSCJAG00000015401	1 retrocopy	retro_cjac_1749,
Macaca mulatta	ENSMMUG00000013980	1 retrocopy	retro_mmul_2019,
Ictidomys tridecemlineatus	ENSSTOG00000009459	1 retrocopy	retro_itri_1696 ,
Tursiops truncatus	ENSTTRG00000001154	1 retrocopy	retro_ttru_1573,