RetrogeneDB ID: retro_itri_615

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393306.1:8185756..8187324(+)
• Located in intron of: ENSSTOG00000008771

Retrocopy information

• Ensembl ID: ENSSTOG00000020155
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000010889
• Aliases: None
• Description: None

Sequence

>retro_itri_615
CAAGATAAAATTCCTTCAGAAAAAGAAATGAAAAAGAGCACACAGGATGAAGCTGTGGGGAGAAGGTTCAAGATCACAAT
TCCTTATGGGATGAAGTATAATAAGACTTGGCTAATGAATTCAATCCTGAGCCATTGCTGTGTCCCCTTTACACCAATTG
ATTTCCACTATATCAAAAATCGGGCCCAATTTTTTGTCCAGGATGCTAGTACTGCCTCTGCATTGAAAGATGTCAACTGC
AAATTTGTGATGAGGAAAATCAAAAGATATCGATCTTTGTCAATCCCTGTATTGAACCAAATACCTTGCAGAATAAATTC
ACTCCAGAAAAAATGGAGAAGCTAATGCTAGTGATGAACAAACGATATGATGTCTCACAGCAAGCCCTTGATCTCCAGAA
GCTCCGCTTTGACCCAGACTTGATGGAGCATGACATTGACATGATCCTAAACCGAAGACAGTGTATGTTTTCTACCCTTC
AGATCATTGAAAGGAATTTCCCTGAGCTGTTGTCCTTGAACTTGTGTAACAACAAACTATACTGGCTGGATGGCCTATCT
GACATTGTAGAGAAAGCCCCCCAAGTCAAGATCCTGAACCTCTCCAAAAATGAGCTGAGGACCTCCAAGGAGTTGGTCAA
GCTGAAAGGGATGAAGCTGGAAGAGCTATGGCTAGAAGGAAACCCCTTGTGCAGTGACTTCCCAGAGCAGTCTGCTTATG
TAAGTGCTATCCAGGATTGTTTCCTCAATTTGTTACGCCTGGATGGCCAGGAGTTACCAGAATCAATTGGAATTGACAAT
GAAACACCTGAAATAATAAAACCTTGTAAGGAAAGCTATAAAGGATATGATAATCTGAAGAGTCTAGTATTGCAATTCCT
GCTTCAGTATTACCTCATTTATGACTATGGAGATCGACAGGGTCTCATTGATGCTTACCATGATGAGGCCTGCTTCTCCC
TGACCATTCCCTTCAACCCTGAGGACCCAGACTCGAATAGCTTGGAAGAGTATTTCAAGGATAATAGAAATATAAAGAAG
CACAAGGACCCCTTTTTGCAGATGCAGCTGCTAAAGCACACAAAATGTGACATTGTGAACTGCCTCAGTGTATTGCCCAA
AACTCAGCATGATTTTAACTCGTATGTGATAGACCTATGTGTCCAGACAGAAATGATGCTCTGTTTTTCTGTCAATGGAT
TGTTCAAGGAAGTGGAAGGAAAGTCTCAGGGTTCTGTTTGTGCCTTCACCTGGACCTTCATCTTAACTTCTGGCAGCAAT
TCCAGTCTGTGCATCGTGAATGATGAGATGATTGTGAGGAATGCCAGCCCCAAAGAGAACCGAGAGCGCCTTCTCCATCC
CCATGCTTACACCCTCCTCCAACTATGTGCCTGACCTCTACCAGGAGCAGCAGGGAATAGCACAGCCTTTCTCCACCAAG
TCTGAGATGCAGAGCCTTGAGCGCTCTCAGAAGTGCCTTGAAGACAAGGAGGAGAACTAACCAGAGTTGGTCAGGTCTTC
ACTGTGTTCCAGGTCAAGAATCCACAGGAGGCCTCAAACAGATGCCCT

Alignment

ORF - retro_itri_615 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.99 %
• Parental protein coverage: 85.34 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KDTKPEERETGEDTQGKTMGNWFKVTIPHGRKYDKAWLMNTVQSHCIVPFTPVDFHYIRNQARFFVQDVK
          .D..P.E.E....TQ....G..FK.TIP.G.KY.K.WLMN...SHC.VPFTP.DFHYI.N.A.FFVQD..
Retrocopy QDKIPSEKEMKKSTQDEAVGRRFKITIPYGMKYNKTWLMNSILSHCCVPFTPIDFHYIKNRAQFFVQDAS

Parental  TASALKDISYK-ICDEENRKISVFVNTSAVPYSMQNKFTPEQMEQLKLTMSKRYDVSQQVLNLQKLRFDS
          TASALKD...K.ICDEEN.KIS.FVN....P...QNKFTPE.ME.L.L.M.KRYDVSQQ.L.LQKLRFD.
Retrocopy TASALKDVNCK<ICDEENQKISIFVNPCIEPNTLQNKFTPEKMEKLMLVMNKRYDVSQQALDLQKLRFDP

Parental  DLVGHDIHMILNRRNCMFATLQIIESNFPELLSLNMQNNKLYQLDGLSDIIEKAPKVKILNLSKNELRTT
          DL..HDI.MILNRR.CMF.TLQIIE.NFPELLSLN..NNKLY.LDGLSDI.EKAP.VKILNLSKNELRT.
Retrocopy DLMEHDIDMILNRRQCMFSTLQIIERNFPELLSLNLCNNKLYWLDGLSDIVEKAPQVKILNLSKNELRTS

Parental  KELDKLKGLKLEELWLEGNPLCSTFPDQSAYVSAIQDCFPNLLRLDGQEISTPVVIDPDAPKLIKPCKES
          KEL.KLKG.KLEELWLEGNPLCS.FP.QSAYVSAIQDCF.NLLRLDGQE......ID...P..IKPCKES
Retrocopy KELVKLKGMKLEELWLEGNPLCSDFPEQSAYVSAIQDCFLNLLRLDGQELPESIGIDNETPEIIKPCKES

Parental  YKGSETLKNLVLQFLQEYYLIYDYGDRQGLLSAYHDEACFSLTIPFNPKDPAPNSLCKYFKYSRNMKKLK
          YKG...LK.LVLQFL..YYLIYDYGDRQGL..AYHDEACFSLTIPFNP.DP..NSL..YFK..RN.KK.K
Retrocopy YKGYDNLKSLVLQFLLQYYLIYDYGDRQGLIDAYHDEACFSLTIPFNPEDPDSNSLEEYFKDNRNIKKHK

Parental  DSNMRRQLLKHTKHDIVDYLSVLPKTEHDFSCLMVDMWFQTETMLCFSVNGVFKEAEGKSQGCVHAFTRT
          D.....QLLKHTK.DIV..LSVLPKT.HDF.....D...QTE.MLCFSVNG.FKE.EGKSQG.V.AFT.T
Retrocopy DPFLQMQLLKHTKCDIVNCLSVLPKTQHDFNSYVIDLCVQTEMMLCFSVNGLFKEVEGKSQGSVCAFTWT

Parental  FIAIPTNNSSICIMNDELIVRNASRDE-IQSSFSIPMPALFSTSMPTLSQEQQEMVKVFSTQSGMK-LEW
          FI.....NSS.CI.NDE.IVRNAS..E...S.FSIPM....S...P.L.QEQQ.....FST.S.M..LE.
Retrocopy FILTSGSNSSLCIVNDEMIVRNASPKE>TESAFSIPMLTPSSNYVPDLYQEQQGIAQPFSTKSEMQSLER

Parental  SQKCLEDNEWN-YTRAGQVFIMLQTEGKIPEEAFKQLP
          SQKCLED.E.N..TR.GQVF...Q...K.P.EA....P
Retrocopy SQKCLEDKEEN<LTRVGQVFTVFQV--KNPQEASNRCP

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_615 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_615 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Microcebus murinus	ENSMICG00000010798	1 retrocopy	retro_mmur_243,
Sarcophilus harrisii	ENSSHAG00000006407	1 retrocopy	retro_shar_58,
Ictidomys tridecemlineatus	ENSSTOG00000010889	1 retrocopy	retro_itri_615 ,