RetrogeneDB ID: retro_itri_757

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393318.1:11520725..11522016(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GDI2
• Ensembl ID: ENSSTOG00000006449
• Aliases: None
• Description: GDP dissociation inhibitor 2 [Source:HGNC Symbol;Acc:4227]

Sequence

>retro_itri_757
CTGGGCATTGGCCTGATGGAATGTATTCTGTCTGGTATTTTGTCAGTGAATGCAAAGAAGGTTCTTCATATGGATCGAAA
CCCATATTATGGAGGAGAAAGTGCATCTATAACTCCACTGGAAGATTTATACAAAAGATTTAAATTACCAGGACCTCCAC
CAACATCAATGGGGAGAGGAAGAGACTGGAATGTTGATTTAATTCCCAAGTTTTTTATGGCCAACAGTCAGCTGGTTAAG
ATGCTACTTTACACAGAGGTCACTAGCTACCTAGATTTCAAAGTGACTGAAGAGAGCTTTGTTTATAAGGGAGGAAAAAT
CTGCAAGGTTCCTTCCACTCAAGCAGAAGCCCTGGTATCTAGTTTAATGGGACTATTTGAAAAATGTCGCTTCAGAAAAT
TCCTAGTGTATGTTGCCAACTTTGATGAAAAAGATCCTAGAACTTTTGAGGATATCCATCCTAAGAAGACCACAATGCGA
GATGTGTACAAGAAATTTGATTTGGGCCAAGATGTTATAGATTTTACTGGTCATACTCTTGCACTTTATAGAACTGATGA
CTATTTATATCAACCATGTTGTGAAACCATTAATAGAATTAAACTTTACCGTTAGTCTTTGGCAAGATATGGCAAAAGCC
CATACCTTTATCCACTTTATGGCCTTGGAGAATTGCCACAAGGATTTACAACGCTGAGTGCTATTTATGGAGGTACTTAT
ATGTTGAATAAACCAATCGAATAAATCATTGTGCAAAATGGAAAAGTGGTTGGTGTAAAGTCTGAAAGAGAGATTGCTCG
CTGTAAGCAGCTCATCTGGGACCCCAGCTATGTAAAAGATCGAGTAGAAAAAGTGGGCCTGGTCATCAGAGTTTTATGCA
TCCTCAGCCACCCCATCAACGATGCCAACTCCTGTCAGATGATTATTCCACAGAACCAAGTCAATCGAAAGTCTGATATC
TATGTTTGCATGATCTCCTCTGCACACAATGTGGCAGTGCAAGGAAAGTACATGGCCATTGTCAGTACAACTGTGGAAAC
CAAGGAACCTGAAAAAGAAATCAGACCAGCTTTGGAGCTCTTGGAGCCAATTGAACAAAAATTTGTTAGCATCAGACCTT
CTTGTACCAAAATATTTGGGAGAAGAGAGCCAGATCTTTATTTCCTGCACATATTATGCCACAACTCACTTTGAGACAAC
CTGTGATGACATTAAAGACATCTATAGGAGGATGACAGGATATGAGTTTGATTTTGAGGAAATGAAGCACAAGAAAAATG
ACATCTGTGGG

Alignment

ORF - retro_itri_757 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.97 %
• Parental protein coverage: 97.53 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LGTGLTECILSGIMSVNGKKVLHMDRNPYYGGESASITPLEDLYKRFKLPGPPPTSMGRGRDWNVDLIPK
          LG.GL.ECILSGI.SVN.KKVLHMDRNPYYGGESASITPLEDLYKRFKLPGPPPTSMGRGRDWNVDLIPK
Retrocopy LGIGLMECILSGILSVNAKKVLHMDRNPYYGGESASITPLEDLYKRFKLPGPPPTSMGRGRDWNVDLIPK

Parental  FLMANGQLVKMLLYTEVTRYLDFKVTEGSFVYKGGKIYKVPSTEAEALASSLMGLFEKRRFRKFLVYVAN
          F.MAN.QLVKMLLYTEVT.YLDFKVTE.SFVYKGGKI.KVPST.AEAL.SSLMGLFEK.RFRKFLVYVAN
Retrocopy FFMANSQLVKMLLYTEVTSYLDFKVTEESFVYKGGKICKVPSTQAEALVSSLMGLFEKCRFRKFLVYVAN

Parental  FDEKDPRTFEGIDPKKTTMRDVYKRFDLGQDVIDFTGHALALYRTDDYLDQPCCETINRIKLYSESLARY
          FDEKDPRTFE.I.PKKTTMRDVYK.FDLGQDVIDFTGH.LALYRTDDYL.QPCCETINRIKLY..SLARY
Retrocopy FDEKDPRTFEDIHPKKTTMRDVYKKFDLGQDVIDFTGHTLALYRTDDYLYQPCCETINRIKLYR*SLARY

Parental  GKSPYLYPLYGLGELPQGFARLSAIYGGTYMLNKPIEEIIVHNGKVVGVKSEGEIARCKQLICDPSYVKD
          GKSPYLYPLYGLGELPQGF..LSAIYGGTYMLNKPIE.IIV.NGKVVGVKSE.EIARCKQLI.DPSYVKD
Retrocopy GKSPYLYPLYGLGELPQGFTTLSAIYGGTYMLNKPIE*IIVQNGKVVGVKSEREIARCKQLIWDPSYVKD

Parental  RVEKVGQVIRVICILSHPIKNTNDANSCQIIIPQNQVNRKSDIYVCMISSAHNVAAQGKYIAIVSTTVET
          RVEKVG.VIRV.CILSHPI...NDANSCQ.IIPQNQVNRKSDIYVCMISSAHNVA.QGKY.AIVSTTVET
Retrocopy RVEKVGLVIRVLCILSHPI---NDANSCQMIIPQNQVNRKSDIYVCMISSAHNVAVQGKYMAIVSTTVET

Parental  KEPEKEIRPALELLEPIEQKFVSISDLLVPKDLGR-ESQIFISRTYDATTHFETTCDDIKDIYKRMTGSE
          KEPEKEIRPALELLEPIEQKFVSI......K..GR.ESQIFIS.TY.ATTHFETTCDDIKDIY.RMTG.E
Retrocopy KEPEKEIRPALELLEPIEQKFVSIRPSCT-KIFGR>ESQIFISCTYYATTHFETTCDDIKDIYRRMTGYE

Parental  FDFEEMKRKKNDIYG
          FDFEEMK.KKNDI.G
Retrocopy FDFEEMKHKKNDICG

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_757 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_757 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.

---

Parental genes homology:

Parental genes homology involve 10 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005316	1 retrocopy	retro_btau_1208,
Canis familiaris	ENSCAFG00000005223	2 retrocopies	retro_cfam_2196, retro_cfam_886,
Callithrix jacchus	ENSCJAG00000020512	2 retrocopies	retro_cjac_1168, retro_cjac_3115,
Cavia porcellus	ENSCPOG00000013449	1 retrocopy	retro_cpor_696,
Gorilla gorilla	ENSGGOG00000003623	1 retrocopy	retro_ggor_2590,
Mus musculus	ENSMUSG00000021218	2 retrocopies	retro_mmus_2971, retro_mmus_360,
Oryctolagus cuniculus	ENSOCUG00000005367	1 retrocopy	retro_ocun_69,
Ictidomys tridecemlineatus	ENSSTOG00000006449	1 retrocopy	retro_itri_757 ,
Ictidomys tridecemlineatus	ENSSTOG00000022111	1 retrocopy	retro_itri_870,
Tupaia belangeri	ENSTBEG00000011523	1 retrocopy	retro_tbel_644,