RetrogeneDB ID: retro_itri_1325

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393441.1:2564977..2565638(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NT5C3A
• Ensembl ID: ENSSTOG00000026363
• Aliases: None
• Description: 5'-nucleotidase, cytosolic IIIA [Source:HGNC Symbol;Acc:17820]

Sequence

>retro_itri_1325
AAAGAAAAAAGATGCATAACATGTTATAATATCATTGACAAGTGTAAGCCAGTTACAGATGAGTGTTGAAATGGTTATTA
CCAGTAAAGAAACAACAACATGTTTCTGAAGTTGATTGTATGCTTACTGTAGAAAAGAAGAATGCTTGGGTGTTACAATG
GTACACTAAATCACATAGTTTTCATGTTGAACAAGCTATACCAAAAAGCTGAACTTTATAAATTACAGAAAAATCTGATG
TTTTACTCAAAGAAGGGTAAGATAATTTCTAGGATAAGCTCCAAAAACATAAAGTGTGCACATTTTTGGCTGGTATTAGT
GATTTACTAAAGGAAGTTATGCATTGAGTTTCTATTTATCATCCAGATGTTAAAGTAGTGTCCAATTTCACAAATTTTGA
TGAAAATGGGGTACTCAGTAGACTTGAAGGAAAACTAATTTGTATATTTAACTAACATAATGGTGTCTTGAAGAATATAG
AATATCTCAGCCTACTAAACAACAATAATAACATAATTCTACTGAGAGACTTGTAAAGGGACTTAAGGAAGCAGATAGAG
TAGTCAATGTTGAATACATTTTGAAAATAAGATGTCTAAATTACAGTGTGGATGAGCTTTTAGAAAAGCACAGATACTCT
AATATAGTTTTAGTAAAAAAA

Alignment

ORF - retro_itri_1325 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.42 %
• Parental protein coverage: 67.67 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KGKRCPTSHNIIDNCKLVTDEC-RKKLLQLKEQYYAIEVNPGLTVEEKYPHMVEWYSKSHSLIVEQGIPK
          K.KRC.T..NIID.CK.VTDEC..K.LL..K.Q....EV...LTVE.K......WY.KSHS..VEQ.IPK
Retrocopy KEKRCITCYNIIDKCKPVTDEC<LKWLLPVKKQQHVSEVDCMLTVEKKNAWVLQWYTKSHSFHVEQAIPK

Parental  AKIKEIVEESDVMLKEGYEDFFDKLKQYNIPVFIFSAGIGDVLEEVLRQAGVYHPNIKVVSNFMDFDENG
          .....I.E.SDV.LKEG...F.DKL.......F...AGI.D.L.EV......YHP..KVVSNF..FDENG
Retrocopy S*TL*ITEKSDVLLKEG*DNF*DKLQKHKVCTFL--AGISDLLKEVMH*VSIYHPDVKVVSNFTNFDENG

Parental  ILKGFKGELIHVFNKHDGALKNTDYFIQLKDNSNIILLGDSEGD-LKMADGVANVEHILKIGYLNDKVDE
          .L....G.LI..FN.H.G.LKN..Y...L..N.NIILL.D...D.LK.AD.V.NVE.ILKI..LN..VDE
Retrocopy VLSRLEGKLICIFN*HNGVLKNIEYLSLLNNNNNIILLRDL*RD<LKEADRVVNVEYILKIRCLNYSVDE

Parental  LLEKYMDSYDIVLVKE
          LLEK...S..IVLVK.
Retrocopy LLEKHRYS-NIVLVKK

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_1325 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1325 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 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006624	1 retrocopy	retro_amel_875,
Bos taurus	ENSBTAG00000016709	1 retrocopy	retro_btau_1465,
Canis familiaris	ENSCAFG00000003154	1 retrocopy	retro_cfam_1295,
Equus caballus	ENSECAG00000011777	1 retrocopy	retro_ecab_1118,
Homo sapiens	ENSG00000122643	1 retrocopy	retro_hsap_3084,
Gorilla gorilla	ENSGGOG00000028164	1 retrocopy	retro_ggor_2119,
Mustela putorius furo	ENSMPUG00000005546	2 retrocopies	retro_mputfur_1175, retro_mputfur_577,
Pteropus vampyrus	ENSPVAG00000013182	2 retrocopies	retro_pvam_148, retro_pvam_706,
Rattus norvegicus	ENSRNOG00000005981	1 retrocopy	retro_rnor_632,
Sus scrofa	ENSSSCG00000022912	1 retrocopy	retro_sscr_540,
Ictidomys tridecemlineatus	ENSSTOG00000026363	2 retrocopies	retro_itri_1325 , retro_itri_682,