RetrogeneDB ID: retro_itri_922

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393344.1:8265446..8266246(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CTH
• Ensembl ID: ENSSTOG00000000202
• Aliases: None
• Description: cystathionase (cystathionine gamma-lyase) [Source:HGNC Symbol;Acc:2501]

Sequence

>retro_itri_922
GCAACACTGGATGGGGCCAAGTACAGTTTGGCCTTTGCTGCGGGTTTAGCAGCCACTATGACTATTACTCATCTTTTAAA
AGCAGGAGACCAAATTATTTGCATGGATGATGTGTGTGGAGGTATGAACAGGTACTTCAGGCAGGTGGTTGCTGAATTTG
GATTAAAGATTTATTTTGTTGAATGTTCCAAAATCAAATTGCTAGAGACAGCAAATACACCAGAAACCAAGCTGGTTTGG
ATTGAAACCCCCACAAACCTGAAGCTTGAAGCTGATTGACATTGAAGCCTGCGTACATACTGTCCAAAAGCATGGAGACA
TTTTTTTTGGCTGTGGAAAACAATTTTATGTTGGCATATTTCCAGCGGCCTTTGGCTCTGGGAGCTGATATTTTTATGTA
TTCTGCAACAAAACACATGAATGGCCACAGTGATGTTGGAATGGGTTTAGTGTGTGTTAATTCTGAAGATCTCCAAGGTA
GAATTCATTTCTTGCAAAATGCTCTTGGAGCAATTCCATCTCCTATTGACTGTTACCTCTGCCATTGAGGCCTGAAGACT
CTGAAAATCCAAATGGAGAAGCATTTCAAAAATGGAATGGCTCTTGCCCAATTCCTAGAATCTAATCCCCGGATAGAAAA
AGTCGTTTATCCTGGTTTGCTCTCCCATCCACAGCGTGAGTTGGCAAAGTGGCAGGGCACAGGTTGCCCCAAGATGATCA
CTTTTTTATTTTTTATTAAGGGCACTCTTCAACATGCTGAGACTTTCCCCAAGAACCTAAAGTTATTTACCCTTAAAGAT

Alignment

ORF - retro_itri_922 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.87 %
• Parental protein coverage: 66.5 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AALDGAKYSLAFASGLAATMTITHLLKAGDQIICMDDVYGGTNRYFRQVAPKFGLKLSFVDCSKTKLLEA
          A.LDGAKYSLAFA.GLAATMTITHLLKAGDQIICMDDV.GG.NRYFRQV...FGLK..FV.CSK.KLLE.
Retrocopy ATLDGAKYSLAFAAGLAATMTITHLLKAGDQIICMDDVCGGMNRYFRQVVAEFGLKIYFVECSKIKLLET

Parental  AITPETKMVWIETPTNP-NLKLIDIEACAHTVHKYGNIIL-VVDNTFMSAYFQRPLALGADICMYSATKY
          A.TPETK.VWIETPTN...LKLIDIEAC.HTV.K.G......V.N.FM.AYFQRPLALGADI.MYSATK.
Retrocopy ANTPETKLVWIETPTNL>SLKLIDIEACVHTVQKHGDXXX>AVENNFMLAYFQRPLALGADIFMYSATKH

Parental  MNGHSDVVMGIVSVNSEDIHDRLRFLQNALGAVPSPMDCYLCIRGLKTLQIRMEKHFKNGMAVAQFLESN
          MNGHSDV.MG.V.VNSED...R..FLQNALGA.PSP.DCYLC..GLKTL.I.MEKHFKNGMA.AQFLESN
Retrocopy MNGHSDVGMGLVCVNSEDLQGRIHFLQNALGAIPSPIDCYLCH*GLKTLKIQMEKHFKNGMALAQFLESN

Parental  PLIEKVIYPGLPSHPQHELAKRQCTGCSGMI--TFFIKGTLQHAETFLKNLKLFTLAE
          P.IEKV.YPGL.SHPQ.ELAK.Q.TGC..MI.....IKGTLQHAETF.KNLKLFTL..
Retrocopy PRIEKVVYPGLLSHPQRELAKWQGTGCPKMIXXXXXIKGTLQHAETFPKNLKLFTLKD

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_922 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_922 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014791	1 retrocopy	retro_btau_1577,
Latimeria chalumnae	ENSLACG00000000234	1 retrocopy	retro_lcha_42,
Ictidomys tridecemlineatus	ENSSTOG00000000202	1 retrocopy	retro_itri_922 ,