RetrogeneDB ID: retro_rnor_2789

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: X:38033230..38033701(+)
• Located in intron of: ENSRNOG00000025290

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ubl4a
• Ensembl ID: ENSRNOG00000037250
• Aliases: Ubl4a, RGD1563983, Ubl4
• Description: Ubiquitin-like protein 4A [Source:UniProtKB/Swiss-Prot;Acc:B2GV38]

Sequence

>retro_rnor_2789
ATGCAGCCGACCATGAAAGCGCTCCAGGGCAGTGAGTGCAGCCTACAGGAGGCTGAGGACGAGCTAGTGTCTACACTGAA
GCACCTGGTCACAGATAAGCTGAATGTCCCTGTGTGCCAGCAATGTCTGCTGTTCAAGGGCAAGGCCCTAGCAGATGAGA
AGGGACTGTCAGATTACAACATTGGCCCCAACTCTAAACTCAACCTAGTTGTTAAGCCTTGGGAGAAGGTGCTACTGTAA
GAAGGGTCTGCCCAGAGACTGGGCGACTCCCCAGCCATCCCCATCTGGCAGCTGATCTCCAAAGGCCTGGCCCCTCACTT
CAGTATAGGAGATGCCAGCAGGGTCCTGGAACAACTACAGAGGGATTATGACAGGTCCTTGTGCCGCCTAATACTGGATG
ACATCGAATGTTTGGCCAGACGCTTTCTACACCCTGAAGTGACTGAGGCCATGGAAAAGGGGTTCTGCAAA

Alignment

ORF - retro_rnor_2789 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.26 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MQLTVKALQGRECSLQVAEDELVSTLKHLVSDKLNVPVRQQRLLFKGKALADEKRLSDYNIGPNSKLNLV
          MQ.T.KALQG.ECSLQ.AEDELVSTLKHLV.DKLNVPV.QQ.LLFKGKALADEK.LSDYNIGPNSKLNLV
Retrocopy MQPTMKALQGSECSLQEAEDELVSTLKHLVTDKLNVPVCQQCLLFKGKALADEKGLSDYNIGPNSKLNLV

Parental  VKPLEKVLLEEGSAHRLVDSSATPIWQLISKVLARHFSIGDASRVLEQLQRDYDRSLSRLTLDDIERLAS
          VKP.EKVLL.EGSA.RL.DS.A.PIWQLISK.LA.HFSIGDASRVLEQLQRDYDRSL.RL.LDDIE.LA.
Retrocopy VKPWEKVLL*EGSAQRLGDSPAIPIWQLISKGLAPHFSIGDASRVLEQLQRDYDRSLCRLILDDIECLAR

Parental  RFLHPEVTEAMEKGFCK
          RFLHPEVTEAMEKGFCK
Retrocopy RFLHPEVTEAMEKGFCK

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
SRP017611_brain	0.00 RPM	37.82 RPM
SRP017611_kidney	0.00 RPM	27.22 RPM
SRP017611_liver	0.00 RPM	18.36 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2789 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2789 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2789 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000005040	1 retrocopy	retro_acar_123,
Bos taurus	ENSBTAG00000014331	1 retrocopy	retro_btau_195,
Callithrix jacchus	ENSCJAG00000016805	1 retrocopy	retro_cjac_3272,
Ochotona princeps	ENSOPRG00000012645	1 retrocopy	retro_opri_714,
Rattus norvegicus	ENSRNOG00000037250	1 retrocopy	retro_rnor_2789 ,