RetrogeneDB ID: retro_itri_1894

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH396084.1:5044..6117(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MTMR10
• Ensembl ID: ENSSTOG00000008851
• Aliases: None
• Description: myotubularin related protein 10 [Source:HGNC Symbol;Acc:25999]

Sequence

>retro_itri_1894
TCGACTTGCCTTCCAGAGTACTTTGTAGTGCCAAGTTCTTTAGCAGACCAACATCTGAAAATCTTTTTGCATTCTTTTGT
TGGAAGAAGCATGTTACTCTGCTATTAAAGCCACTCAATGGCAGTGCTCTTGTGTGAATAGCCCTCATTAAAGATGTGTT
GCAGCAGAGAAAACTGACCAGAGGATTTGTTATGCAATAACTGAAACTCATCCACAGAGAAGTTATGTTTACAACTCAGG
TTTGGATAAGATCTTGCCTAATGTTCAAGAAATACAGGCGACATTTGTAAAACTTAAGCAACTATGCATTCATGAACCTT
TTGAAGAAATGTAGAGAAATGACTATCTTCACTAGAAAATACTCTGTGGTTAGAATATGTCAGGGCTTTTCTTAAATATT
TAGCAGAACTTGTGTACATGCTAGAAAGCAAACATCTCTCTATAATACTACAAGAGGAGGAGGGAAGAGACTTAAGTTGT
CTTATAGCTTCTCATGTTCAAGTGATGCTGAATCCATATTTTAGGATAATTACTGGATTTCAGAGTCTGCTACAGAAGGA
GTGGCCCATGGCAGGATTTCACTTCCTAAACAGATGCAACCATTTGAGGAGATCAGAAAAAGAGTCTCCCTTATTTTTGC
TGTTCTTGAATCCATGTGGCAACTGTTAGAACAGTACCCAGCAGCCTTTGAGTTTCCTGAGACTTACTTAGCAGTGCTTT
GTGACAGAATCCAGTTCTCACTGTTCAGCACCTTCCTGTTCCACTTTCCTCATCAACAGGTGAAGCAAAGCACAGAATTT
GTTATAAGCAAAAATATCCAATTGGGTGATGAAAAGGGCTTAAAATTCCCTTCAGTTTGGTCTCCTCAGTTCGCAGCAAA
GGACCGCACACTTTCCCACAACCCCTTCTACAATGGAAAGATCACGCCTTGCATACAGAATGGCTCTATCAAGTCTTTTA
AACAAATGAAGAAAAGCTACAGCTCCACACTAAGAGGAATGCCATCTTCCATAAAGAATGAAATCATCAGTGACCAAGAA
TTAGTGCCCAGGAGAATTAACTCATTAACTAAA

Alignment

ORF - retro_itri_1894 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.64 %
• Parental protein coverage: 68.5 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  STCLPEYFVVPSSLADQDLKIFSHSFVGRRMPLWCWSHS-NGSALVRMALIKDVLQQRKI-DQRICNAIT
          STCLPEYFVVPSSLADQ.LKIF.HSFVGR.M.L...SHS.NGSALV..ALIKDVLQQRK..DQRIC.AIT
Retrocopy STCLPEYFVVPSSLADQHLKIFLHSFVGRSMLLCY*SHS<NGSALV*IALIKDVLQQRKL<DQRICYAIT

Parental  KSHPQRSDVYKSDLDKILPNIQEIQAAFVKLKQLCVNEPFEE-TEEKWLSSLENTRWLEYVRAFLKHSAE
          ..HPQRS.VY.S.LDKILPN.QEIQA.FVKLKQLC..EPFEE...EK.LSSLENT.WLEYVRAFLK..AE
Retrocopy ETHPQRSYVYNSGLDKILPNVQEIQATFVKLKQLCIHEPFEE<NVEK*LSSLENTLWLEYVRAFLKYLAE

Parental  LVYMLESKHLSIILQEEEGRDLSCLIASLVQVMLDPYFRTITGFQSLIQKEWVMAGFQFLDRCNHLKRSE
          LVYMLESKHLSIILQEEEGRDLSCLIAS.VQVML.PYFR.ITGFQSL.QKEW.MAGF.FL.RCNHL.RSE
Retrocopy LVYMLESKHLSIILQEEEGRDLSCLIASHVQVMLNPYFRIITGFQSLLQKEWPMAGFHFLNRCNHLRRSE

Parental  KESPLFLLF-LDATWQLLEQYPAAFEFSETYLAVLCDSTRISLFSTFLFNSPHQRVKQSTEFAISKNIQL
          KESPLFLLF.L...WQLLEQYPAAFEF.ETYLAVLCD....SLFSTFLF..PHQ.VKQSTEF.ISKNIQL
Retrocopy KESPLFLLF<LESMWQLLEQYPAAFEFPETYLAVLCDRIQFSLFSTFLFHFPHQQVKQSTEFVISKNIQL

Parental  GDEKGLKFPSVWDWSLQFTAKDRTLFHNPFYIGKSTPCIQNGSMKSFKRTKKSYSSTLRGMPSSIKNGII
          GDEKGLKFPSV..WS.QF.AKDRTL.HNPFY.GK.TPCIQNGS.KSFK..KKSYSSTLRGMPSSIKN.II
Retrocopy GDEKGLKFPSV--WSPQFAAKDRTLSHNPFYNGKITPCIQNGSIKSFKQMKKSYSSTLRGMPSSIKNEII

Parental  SDQELLPRRNSLILK
          SDQEL.PRR.....K
Retrocopy SDQELVPRRINSLTK

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_1894 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1894 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 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012336	1 retrocopy	retro_chof_1162,
Monodelphis domestica	ENSMODG00000011784	2 retrocopies	retro_mdom_1377, retro_mdom_1957,
Ictidomys tridecemlineatus	ENSSTOG00000008851	1 retrocopy	retro_itri_1894 ,
Ictidomys tridecemlineatus	ENSSTOG00000020537	1 retrocopy	retro_itri_1574,