RetrogeneDB ID: retro_itri_1221

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393405.1:439603..440602(-)
• Located in intron of: ENSSTOG00000020211

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000011626
• Aliases: None
• Description: None

Sequence

>retro_itri_1221
CCACCGCCACCCCAGCAGCAGCAGCCGCAGTGCAGCAGGAAGAAGGGATGGCAGCTGAGGCCCGAAGAGCAGTGATGTCC
CCTATGGACGAAGGGTTTCTGAGCCTGGACTCGCCCACCTATGTCCTGTACAGGGACAGAGCAGAATGGGCTGATATAGA
TCCAGTACCACAGAATGATGGTCCAAATCCAGAAGTCCAGATCATCTATAGTGAAAAATTTAGAGATGTTTATGATTATT
TCTTAGCTGTTCTACAGGGTGATGAAAGAAGTGAACGAGCTTTTAAGCTTACCTGGGATGCTATTGAGTTAAATGTTGCC
AATTATGCAGTGTGGCATTTTCAGAGAGTTCTCTTAAAGTCACTTCAAAAGGATCTACATGAGGAAATGAACTACATCAT
TGCAATATTTGAGGAACAGCCCTCAAACCATCAAGTTTGGCACCATAGGCGAGTATTAGTAGAATGGCTAAAAGATCCAT
CTCAGGAACTTGAATTTATTGCTGATATTCTTAACCAGGATGCAAAGAATTACCATGCCTGGTAGCATCCACGATGGGTC
ATTCAGGAATTTAAACGTTGGGATAATGAGCTGCAGTATGTAGACCAACTTCTAAAAGAGGATGTGAGAAATAACTCTGT
CTGGAACCAAAGATACTTTGTCATTTCTAAAACCACTGGCTACAGTGGTCATGGTGTATTGGAAAGAGAAGTCCAATACA
CTCTGGAAATGATCAAACTTGTACCACATAATGAAAGTGCATGGAACTATTTGAAAGGGATTTTGCAGGATTGTGGTCTT
TCCAAATATCCTAACCTGTTAAATCAATTACTTGATTTACAACCAAGTCACAGTTTCCCCTACCTAATTGCCTTTCTTGT
GGATATCTATGATGATATGCTAGAAAACCAATGTGACAACAAAGAGGACATTCTTAATAAAGCATTAGAGTTATGTGAAA
TCCTAGCTAAAGAAAAAGGACACTATAAGAAAGGAATAT

Alignment

ORF - retro_itri_1221 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.25 %
• Parental protein coverage: 87.86 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PPQPHPPPSQ-QQQEEGMAAEAGGAVASPMDDGFLSLDSPTYVLYRDRAEWADIDPVPQNDGPNPVVQII
          PP.P.....Q..QQEEGMAAEA..AV.SPMD.GFLSLDSPTYVLYRDRAEWADIDPVPQNDGPNP.VQII
Retrocopy PPPPQQQQPQ<VQQEEGMAAEARRAVMSPMDEGFLSLDSPTYVLYRDRAEWADIDPVPQNDGPNPEVQII

Parental  YSEKFRDVYDYFRAVLQRDERSERAFKLTQDAIELNAANYTVWHFRRVLLKSLQKDLHEEMNYITAIIEE
          YSEKFRDVYDYF.AVLQ.DERSERAFKLT.DAIELN.ANY.VWHF.RVLLKSLQKDLHEEMNYI.AI.EE
Retrocopy YSEKFRDVYDYFLAVLQGDERSERAFKLTWDAIELNVANYAVWHFQRVLLKSLQKDLHEEMNYIIAIFEE

Parental  QPKNYQVWHHRRVLVEWLKDPSQELEFIADILNQDAKNYHAWQHRQWVIQEFKLWDNELQYVDQLLKEDV
          QP.N.QVWHHRRVLVEWLKDPSQELEFIADILNQDAKNYHAW.H..WVIQEFK.WDNELQYVDQLLKEDV
Retrocopy QPSNHQVWHHRRVLVEWLKDPSQELEFIADILNQDAKNYHAW*HPRWVIQEFKRWDNELQYVDQLLKEDV

Parental  RNNSVWNQRYFVISNTTGYSDRAVLEREVQYTLEMIKLVPHNESAWNYLKGILQDRGLSKYPNLLSQLLD
          RNNSVWNQRYFVIS.TTGYS...VLEREVQYTLEMIKLVPHNESAWNYLKGILQD.GLSKYPNLL.QLLD
Retrocopy RNNSVWNQRYFVISKTTGYSGHGVLEREVQYTLEMIKLVPHNESAWNYLKGILQDCGLSKYPNLLNQLLD

Parental  LQPSHSSPYLIAFLVDIYEDMLENQCDNKEDILNKALELCEILAKE-KDTIRKEY
          LQPSHS.PYLIAFLVDIY.DMLENQCDNKEDILNKALELCEILAKE.KDTIRKEY
Retrocopy LQPSHSFPYLIAFLVDIYDDMLENQCDNKEDILNKALELCEILAKE>KDTIRKEY

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_1221 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1221 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000008272	1 retrocopy	retro_eeur_532,
Homo sapiens	ENSG00000168522	1 retrocopy	retro_hsap_805,
Loxodonta africana	ENSLAFG00000000631	1 retrocopy	retro_lafr_506,
Monodelphis domestica	ENSMODG00000010003	1 retrocopy	retro_mdom_1656,
Nomascus leucogenys	ENSNLEG00000012979	1 retrocopy	retro_nleu_2408,
Sorex araneus	ENSSARG00000009660	1 retrocopy	retro_sara_109,
Ictidomys tridecemlineatus	ENSSTOG00000011626	1 retrocopy	retro_itri_1221 ,