RetrogeneDB ID: retro_itri_523

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393298.1:16085896..16086950(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000011569
• Aliases: None
• Description: None

Sequence

>retro_itri_523
AGCCAGGAGTCCAAAACTACCTACCTGGAGGACCTTCCACCACTCCCTGAGTATGAATTGGCCCCATCCAAGTTAGGAGA
GGAGGTGGATGATGTTTATCTCATTGGAGCTCAAGGATTGCCTTGGTCATGTACTGTGGAAGATGTGCTTAACTTTTTCT
CAGACTGCAGAATCCGCAATAGTGAGAATGGAATACATTTCCTTTTAAATAGAAATGGGAAACGAAGGGATGATGCCTTA
ATTGAAATGGAGTCAGATCAGGATGTGCAGAAAGCCTTAGAAAAGTACTGCATGTGCATGGGTCAGCGATATGTGGAAGT
ATAGGAGATAAATAATGAAGATATGGATGCCTTAATGAAGAGCCTACAGGTCAAGTCGTCACCTGTGGTGAATGATGGTG
TAGTTCGATTAAGAGGACTTCCTTATAGTTGCAATGAGAAAGATATCGTGAACTTCTTTGCAGGATTAAATATAGTGGAC
ATTACTTTTGTAATGGACTATAGAGGGAGAAGAAAAACAGAGGAAGCATATGTGCAGTTTGAAGAACCAGAAATGGCCAA
CCAAGCCTTGTTGAAACACAGGGAAGAAATTGGTAACCGGTATACAGAGATATTTCCAAGCAGAAGGAATGAAGTTCGAA
CCCATGTTGGCTCTCATAGGGAAAGAAAATGGCATCTTCTCCTATTGCTAAGTATATAACTGAGCCAGAAATGGTCTTTG
AAGAACATGAAGTAAATGAAGACATTCGACCCATGACAGGTTTTGAAAATGAGAAGGAGATAGAATTGCCTAAGGAGATG
TCAGAAAAGCTTCCAGAAGGTGTTGATTTTAGAACTACACCTTCATTGCATTTTATCCACATGAGAGGATTACCTTTTCA
AGCTAATGCCCAAGACATTATAAATTTTTTTGTTCCCCTGAAGCCTGTGAGAATCACCATGGAATACATTTCCAGTGGAA
AGGCTACTGGAGAAGCTGATGTGCACTTCGATACCCCTGAGGATGCTGTTGCAGCTATGCTCAAGGATAGGTCCCTGTTC
AGCATAGTTCTATT

Alignment

ORF - retro_itri_523 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.81 %
• Parental protein coverage: 75.05 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TKESKTTYLEDLPPLPEYELAPSKLGEEVDDVYLIRAQGLPWSCTVEDVLNFFSDCRIRNSENGIHFLLN
          ..ESKTTYLEDLPPLPEYELAPSKLGEEVDDVYLI.AQGLPWSCTVEDVLNFFSDCRIRNSENGIHFLLN
Retrocopy SQESKTTYLEDLPPLPEYELAPSKLGEEVDDVYLIGAQGLPWSCTVEDVLNFFSDCRIRNSENGIHFLLN

Parental  RDGKRRGDALIEMESEQDVQKALEKHRMYMGQRYVEVYEINNEDVDALMKSLQVKSSPVVNDGVVRLRGL
          R.GKRR.DALIEMES.QDVQKALEK..M.MGQRYVEV.EINNED.DALMKSLQVKSSPVVNDGVVRLRGL
Retrocopy RNGKRRDDALIEMESDQDVQKALEKYCMCMGQRYVEV*EINNEDMDALMKSLQVKSSPVVNDGVVRLRGL

Parental  PYSCNEKDIVDFFAGLNIVDITFVMDYRGRRKTGEAYVQFEEPEMANQALLKHREEIGNRYIEIFPSRRN
          PYSCNEKDIV.FFAGLNIVDITFVMDYRGRRKT.EAYVQFEEPEMANQALLKHREEIGNRY.EIFPSRRN
Retrocopy PYSCNEKDIVNFFAGLNIVDITFVMDYRGRRKTEEAYVQFEEPEMANQALLKHREEIGNRYTEIFPSRRN

Parental  EVRTHVGSHK-GKKMASSPTAKYITEPEMVFEEHEVNEDIRPMTSFENEKEIELPKEMSEKLPEAVDFGT
          EVRTHVGSH..GKKMASSP.AKYITEPEMVFEEHEVNEDIRPMT.FENEKEIELPKEMSEKLPE.VDF.T
Retrocopy EVRTHVGSHR<GKKMASSPIAKYITEPEMVFEEHEVNEDIRPMTGFENEKEIELPKEMSEKLPEGVDFRT

Parental  TPSMHFVHMRGLPFQANAQDIINFFAPLKPVRITMEYSSSGKATGEADVHFDTHEDAVAAMLKDRS-HVQ
          TPS.HF.HMRGLPFQANAQDIINFF.PLKPVRITMEY.SSGKATGEADVHFDT.EDAVAAMLKDRS..VQ
Retrocopy TPSLHFIHMRGLPFQANAQDIINFFVPLKPVRITMEYISSGKATGEADVHFDTPEDAVAAMLKDRS<PVQ

Parental  HRYI
          H..I
Retrocopy HSSI

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_523 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_523 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 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Nomascus leucogenys	ENSNLEG00000007721	1 retrocopy	retro_nleu_1973,
Ictidomys tridecemlineatus	ENSSTOG00000011569	2 retrocopies	retro_itri_1828, retro_itri_523 ,
Ictidomys tridecemlineatus	ENSSTOG00000011676	1 retrocopy	retro_itri_647,
Ictidomys tridecemlineatus	ENSSTOG00000016376	2 retrocopies	retro_itri_66, retro_itri_78,
Tupaia belangeri	ENSTBEG00000010173	2 retrocopies	retro_tbel_3827, retro_tbel_987,
Tarsius syrichta	ENSTSYG00000008487	1 retrocopy	retro_tsyr_770,