RetrogeneDB ID: retro_mdom_570

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:338883385..338884575(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LACTB
• Ensembl ID: ENSMODG00000011098
• Aliases: None
• Description: lactamase, beta [Source:HGNC Symbol;Acc:16468]

Sequence

>retro_mdom_570
CAAGGTTTAGGTTATATTGATGTAAAAAACAGAATTCCATGTAAACCAGAAACAGTGATGAGAATTGCTAGCATCAGCAA
AAGTCTTACCATGGTGACCATTGCCAAATTATGGGAAGAGGGCAGATTGGATGTTGATATTCCAGGACAGAAATATGTTC
TTGAATTTCCAGAGAAATAATATGAAGGTGAAAAAGTTTCTGTCACTACAAAATTAATGATTTCTCATTTAAGTGGAATT
TGCCACTATGAAAAGGATATGAAAAAAGTAAAAGAAGAGAAGGCTTATAAAGCTTTGAAGATGATGAAAGAAACAATGGA
ATTTAACCAAGACAAAGACTTGAAAGAAACAGGAGGCAAAAGTAATGAAAAGAATGACTTTGCCAAAGTTAAGATACAGC
AAGATAGTGAAGGCAAAGGCTGAAATTCCAAACCTGTCAAGAAGATGAATGATTTTGAACAAGATGAATTATATTTGAAA
GAAAATTTGAAAATTAAATTTAGTTTCTAAGATTATTTTAAAATGATCCTCTGTTCTTTAAACCATGTAGTCAGTTTTTG
TACTCAACTTTTGGATATAGTCTACTGGCATCTGTCATAGAAAGAGCTTCAGGACAGACATTTTTGGACACTATGCAGAA
AATATTCCATGATGTGGATGTGGTGATGACTGTGCAAGAAGAAAATGAGCCAATGATTTACAAGAGAGCAAGGTTTTATG
TTTACAATAAAAAAGGATGTCTTGTCAATACTCCTTATGTGGACAACTTTTATAAATGGGTCATTGGTGCATTTCTTTCT
ATAGTTGGTGATTTTCTTAAATTTGGGAATGTAATACTCTATGGTGACCAAATTGGAATGATTAAAATCTTAAGTGAGAA
GCTTTTGCCAGGGTACCTCAAGCCAGAAACCATGGTCATGATTTGGACTCCTGTGCCAAACACAGAGATGTCTTGGGATA
GAGAAGAAAAATACTCAATGGCCTGGGGTGTGGTGGAAAAGAAGCAGATATATAGCTTCTGTTGGCAACAGCAACATTAT
GCTTCTCACAGTGGAGGGGCAGTGGGTACTAATAATGTCCTGCTAATTCTTCCTGAAGATTTGGAGGTAGAAACTATAGA
TAACAGAATAGCTATTCCCCCAAGAGGAGTGATCATTACCATCATATGTAATATGTAGTCTGTTGGCCTC

Alignment

ORF - retro_mdom_570 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.42 %
• Parental protein coverage: 71.53 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EGLGYADVENRVPCKPETVMRIASISKSLTMVAIAKLWEEGRLDLDIPVQKYVPEFPEKEYEGEKVSVTT
          .GLGY.DV.NR.PCKPETVMRIASISKSLTMV.IAKLWEEGRLD.DIP.QKYV.EFPEK.YEGEKVSVTT
Retrocopy QGLGYIDVKNRIPCKPETVMRIASISKSLTMVTIAKLWEEGRLDVDIPGQKYVLEFPEK*YEGEKVSVTT

Parental  RLLISHLSGIRHYEKDMKKVKEEKAYKALKMTKEAMEFNQDKGLKEIGGKSNEKNDIAKVKIEQDSEGKG
          .L.ISHLSGI.HYEKDMKKVKEEKAYKALKM.KE.MEFNQDK.LKE.GGKSNEKND.AKVKI.QDSEGKG
Retrocopy KLMISHLSGICHYEKDMKKVKEEKAYKALKMMKETMEFNQDKDLKETGGKSNEKNDFAKVKIQQDSEGKG

Parental  RNSKPGKKKNDFEQDELYLKE-KFENSIESLRLFKNDPLFFKPGSQFLYSTFGYSLLAAVIERASGQKFL
          .NSKP.KK.NDFEQDELYLKE.KFEN.I..LRLF.NDPLFFKP.SQFLYSTFGYSLLA.VIERASGQ.FL
Retrocopy *NSKPVKKMNDFEQDELYLKE<KFEN*I*FLRLF*NDPLFFKPCSQFLYSTFGYSLLASVIERASGQTFL

Parental  DYMQKIFHDLDMVTTVQEENEPMIYNRARFYVYNKKGRLVNTPYVDNSYKWAGGGFLSTVGDLLKFGNAM
          D.MQKIFHD.D.V.TVQEENEPMIY.RARFYVYNKKG.LVNTPYVDN.YKW..G.FLS.VGD.LKFGN..
Retrocopy DTMQKIFHDVDVVMTVQEENEPMIYKRARFYVYNKKGCLVNTPYVDNFYKWVIGAFLSIVGDFLKFGNVI

Parental  LYGYQIGMIKNLSEKLLPGYLKPETMVMIWTPVPNTEMSWDREGKYAMAWGVVEKKQTHGSCRQQRHYAS
          LYG.QIGMIK.LSEKLLPGYLKPETMVMIWTPVPNTEMSWDRE.KY.MAWGVVEKKQ....C.QQ.HYAS
Retrocopy LYGDQIGMIKILSEKLLPGYLKPETMVMIWTPVPNTEMSWDREEKYSMAWGVVEKKQIYSFCWQQQHYAS

Parental  HTGGAVGASSVLLILPEDLEVETTDNRMTIPPRGVIVTIICNMQSVGL
          H.GGAVG...VLLILPEDLEVET.DNR..IPPRGVI.TIICNM.SVGL
Retrocopy HSGGAVGTNNVLLILPEDLEVETIDNRIAIPPRGVIITIICNM*SVGL

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	32.30 RPM
SRP007412_cerebellum	0.00 RPM	24.16 RPM
SRP007412_heart	0.00 RPM	41.07 RPM
SRP007412_kidney	0.00 RPM	60.57 RPM
SRP007412_liver	0.00 RPM	43.30 RPM
SRP007412_testis	0.00 RPM	23.18 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_570 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_570 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000017373	1 retrocopy	retro_btau_1569,
Monodelphis domestica	ENSMODG00000011098	1 retrocopy	retro_mdom_570 ,