RetrogeneDB ID: retro_mdom_1663

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 6:91604282..91605223(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNX21
• Ensembl ID: ENSMODG00000013675
• Aliases: None
• Description: sorting nexin family member 21 [Source:HGNC Symbol;Acc:16154]

Sequence

>retro_mdom_1663
CTCTCCTCTCACCTTCTGCAACACCTGTCGCACATCCTACCTCTAACAGGAGAGGGCCCTGGAAATCCAACTGAGGAATT
CCCAGAGAATTCAGAGCTTGAGGATGATGAAACCCAGGTCTTATCCTCATGCCTCAGTGGCACCCTCAGCTTCTCTGGCA
CTGGATATAATGAAGATGAAGAGGAAGTGGAGAAAAACAGGGATTCTCTAGAATGAGGGGCTTCCCTGTGCTGAAGGCTT
ATGAGTCTTGGAGAGAATGGCCCTTGGGAGGATAGAGATTGGAGTGCCCAATTAGATGGGCCACAAGATAGTAAACTCTA
GACTGAAAAACTGTAAGACTTCTGGAAAAATTCAAGAAGTAACCTAGTTCTCCAGTGGCTGCTCTTTGAAGTGACTAATG
CCAATGTCATCAATGAGACATCCTTCAAGTACATGCTCTGCATCATCACCCTGAGAGGCACTAGGTCAAAGTGTGTGCCC
ACCCAGATTTCCTGGCTCTACTCAACCTTTGAACATCCACACTTTCAAATTCAACAACAATTCCATGGGCTGATGGCTGT
GGTTTCCTTCTCTTAAAATGCCTATGGTGCAATTTTCCTGCTGAGAGCATTGCTTGATGCAGCAGGGCCTTTAAAAAATT
TCTGGGGCACCTGCAGGCTGTGCCTGAGCTTCATCAGGCAATAGACCTCCAGGACATCTTCATTCTGCCCCAGCTGAGAT
GGGTGCAAAGGCTCACTTGCACCAGACTCTACCATGAGGCACTTGGGCTCTGAACTAATGCCTGTTGCCTGAAAACCTAA
TTGGGCACTACAGTTGGTGCCCATTGGACACTGTTGACATTGGTAGACCTAGCTGTGTGCCACCAAGACCTGGAGTAGCC
CAGTGAGTCTTGGTTTAGTTGTGAACAGGCTCTTTAGCTGCTAGGGGCTAGTGATTCCCAT

Alignment

ORF - retro_mdom_1663 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.44 %
• Parental protein coverage: 85.48 %
• Number of stop codons detected: 9
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MASRLLHRLRHALTGEGSGEPTPSAEAEEFPESSELEEDDTEGLSTRLSGTLSFTSTEDEEEEEEDEENG
          ..S.LL..L.H.L...G.G...P....EEFPE.SELE.D.T..LS..LSGTLSF..T...E.EEE.E.N.
Retrocopy LSSHLLQHLSHILPLTGEGPGNPT---EEFPENSELEDDETQVLSSCLSGTLSFSGTGYNEDEEEVEKNR

Parental  DPLGSGAALGQRLKSPGEDSPGEEGDRNPPSDGPRGSNLLTRQLQDFWKKSRSNLVPQRLLFEVTSANVI
          D.L..GA.L..RL.S.GE..P.E..D.....DGP..S.L.T..L.DFWK.SRSNLV.Q.LLFEVT.ANVI
Retrocopy DSLE*GASLC*RLMSLGENGPWEDRDWSAQLDGPQDSKL*TEKL*DFWKNSRSNLVLQWLLFEVTNANVI

Parental  NEPPSKYVLYTIALIGPGPQEHVPAQISRRYSDFERLHRQLRQQFRGPMAAVSFP-RKRLRRNFTAETIA
          NE...KY.L..I.L.G......VP.QIS..YS.FE..H.Q..QQF.G.MA.VSF...K.L..NF.AE.IA
Retrocopy NETSFKYMLCIITLRGTR-SKCVPTQISWLYSTFEHPHFQIQQQFHGLMAVVSFS<LKCLWCNFPAESIA

Parental  RRSRAFEQFLGHLQAVPELRQAPDLQDFFILPELRRAQRLTCTGLYREALGLWTNAWRLQTQLGTTVGAH
          ..SRAF..FLGHLQAVPEL.QA.DLQD.FILP.LR..QRLTCT.LY.EALGL.TNA..L.T.LGTTVGAH
Retrocopy *CSRAFKKFLGHLQAVPELHQAIDLQDIFILPQLRWVQRLTCTRLYHEALGL*TNACCLKT*LGTTVGAH

Parental  RTLLTLVGLAVCHQELEQPSEARLSCEQALQLLGDSDSH
          .TLLTLV.LAVCHQ.LE.PSE...SCEQAL.LLG.SDSH
Retrocopy WTLLTLVDLAVCHQDLE*PSESWFSCEQAL*LLGASDSH

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain	0.00 RPM	43.15 RPM
SRP007412_cerebellum	0.00 RPM	60.07 RPM
SRP007412_heart	0.00 RPM	104.46 RPM
SRP007412_kidney	0.00 RPM	42.14 RPM
SRP007412_liver	0.00 RPM	17.62 RPM
SRP007412_testis	0.00 RPM	62.27 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1663 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1663 was not experimentally validated.

Homology

Retrocopy orthology:

Monodelphis domestica 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000013675	1 retrocopy	retro_mdom_1663 ,