RetrogeneDB ID: retro_itri_1840

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH394009.1:19245..20009(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000021338
• Aliases: None
• Description: None

Sequence

>retro_itri_1840
ATTAACAAATGTAAAAATTACTGTGAAGTACTTGGAGTTACAAAAGATGCTGGTGATGAAGATTTGAAAAAAGCTTATAG
AAAGCTTGCTTTGAAGTTTCATCCAGACAAAAACCATGCATCTGGAGCAACAGATGCTTTTAAAAAGATTGGAAATGCTT
ATGCTGTTTTAAACAATCCAGAAAAACGAAAACAGTGTATCTCACAGGCAGTGAAGAACAAGCATACAATCACCAAGCCA
ATGGCAGATTTAATTTCCATAGAGGCTGTGAAGCTGATATAACTCCAGAAGACTTGTTCAATATATTTTTTGGTGGTGGA
TTTCCTTCAGATAGTGTACACTCATTTTCAAATGTCCGAGCTGGTTATAGCCATCAACATCAGCATTGACATAGTGGACA
TGAAAGAGAAGAAAAAGGAGAGAGGGAGGTCTTTCTGTGTTTATCCAGCTGATGCCCATTATCCTACTGAACCTTGTGTC
ATTATTAGCCAACTGGTGGTCTCAAATACTCCTTATTCCTTATATCCCAGATCTGGATCAGAGCAAACCATTAAAATGCA
AACAGAAAATTTGGGCCTTGTTTACTACATCAACAACGACTTTAAAAATGAATATAAAGAAATGTTATTACCAAAGGTTA
AAAAAAGAGTGTAGAAGAAGATTATATGACTAATATTCGAAATAATATCTGGAAAGAAAGCAAAAAACAGATATGCAGTA
TGCAGCAAAAGTGTACTGTGATGATCGACTCCGAAGGAAGGCAG

Alignment

ORF - retro_itri_1840 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.46 %
• Parental protein coverage: 91.7 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  INKCKNYYEVLGVTKDAGDEDLKKAYRKLALKFHPDKNHAPGATDAFKKIGNAYAVLSNPEKRKQ-YDLT
          INKCKNY.EVLGVTKDAGDEDLKKAYRKLALKFHPDKNHA.GATDAFKKIGNAYAVL.NPEKRKQ...LT
Retrocopy INKCKNYCEVLGVTKDAGDEDLKKAYRKLALKFHPDKNHASGATDAFKKIGNAYAVLNNPEKRKQ<VYLT

Parental  GSEDQACNHQNNGRFNFHRGCEADITPEDLFNIFFGGGFPSGSVHSFSNGRAGYSHQHQHRHSGHEREEE
          GSE.QA.NHQ.NGRFNFHRGCEADITPEDLFNIFFGGGFPS.SVHSFSN.RAGYSHQHQH.HSGHEREE.
Retrocopy GSEEQAYNHQANGRFNFHRGCEADITPEDLFNIFFGGGFPSDSVHSFSNVRAGYSHQHQH*HSGHEREEK

Parental  -RGDGGFSVFIQLMPIIVLILVSLL-SQLMVSNPPYSLYPRSGSGQTIKMQTENLGVVYYVNKDF-KNEY
          .R..GG.SVFIQLMPII.L.LVSLL.SQL.VSN.PYSLYPRSGS.QTIKMQTENLG.VYY.N.DF.K...
Retrocopy <RREGGLSVFIQLMPIILLNLVSLL<SQLVVSNTPYSLYPRSGSEQTIKMQTENLGLVYYINNDF>KMNI

Parental  KGMLLQKVE-KSVEEDYVTNIRNNCWKE-RQQKTDMQYAAKVYRDDRLRR
          K....Q....KSVEEDY.TNIRNN.WKE...Q...MQ....V..D...R.
Retrocopy KKCYYQRLK>KSVEEDYMTNIRNNIWKESKKQICSMQQKCTVMIDSEGRQ

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_1840 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1840 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 8 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000012468	1 retrocopy	retro_acar_144,
Homo sapiens	ENSG00000164031	1 retrocopy	retro_hsap_1583,
Monodelphis domestica	ENSMODG00000020687	2 retrocopies	retro_mdom_1398, retro_mdom_752,
Nomascus leucogenys	ENSNLEG00000013668	2 retrocopies	retro_nleu_1761, retro_nleu_2409,
Otolemur garnettii	ENSOGAG00000005340	1 retrocopy	retro_ogar_120,
Pongo abelii	ENSPPYG00000014956	3 retrocopies	retro_pabe_1304, retro_pabe_982, retro_pabe_983,
Pan troglodytes	ENSPTRG00000016311	1 retrocopy	retro_ptro_1066,
Ictidomys tridecemlineatus	ENSSTOG00000021338	1 retrocopy	retro_itri_1840 ,