RetrogeneDB ID: retro_rnor_2871

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: X:132603372..132604470(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Dmtf1
• Ensembl ID: ENSRNOG00000005908
• Aliases: None
• Description: Cyclin-D-binding Myb-like transcription factor 1 [Source:UniProtKB/Swiss-Prot;Acc:Q66HG1]

Sequence

>retro_rnor_2871
AGATCTAATTACAGTAACCTGAACTGGAAACAGAGTGGGGGAACTGAGTGGACCAAGGAAGATGAAATCAATCTCATCCT
CAGGATAGCTGAGCTTGATGTAGCTGATGAAAATGACATAAACTGGGATCTTCTAGCTGAGGGATGGAGCAGTGTTCGTT
CACCACAGTGGCTTCGAAGTAAACGGTGGGCCATCAAAAGGCAAATCGCAAACCATAAGGATGTTTCGTTTCCTGCTTCA
ACAGACTCCCCTGCTGCTTCTGTTGACTCAGAAACAATAACACTAAACAGTGGAACACTACAAACATTTGAGATTCTTCC
ATCTTTCCATTTACAGCCTACTGGTACTCCAGGCACCTACCTTCTTCAAACAAGCTCAAGTCAAGGCCTTCCCCTAACAC
TGACCACAAGTCCCACAGTAACCCTGGCAGCTCCTGCTTCTCCTGAATAGATCATTGTTCATGCTTTATCCCCGGAACAT
TTGTTGAACACAAGTGACAATGTCACAGTACAGTGTCACACACCAAGAGTCATCATTCAAACTGTTGCTACAGAGGACAT
CGCTTCTTCAATATCCCAAGCAGAACTGACAGCTGATAGTGATTTTCATTCATCTGATTTTCCTGAGCCTCCAGATGCAC
TAGAAGCAGACACTTTCCCAGATGAAATTCCTCGGCCTAAGATGACTATACAACCATCATTTAATAATGCTCATGTGTCT
AAATACAGTGACCAAAATAGCACAGAACTGATGAATAGTGTCATGGTCAGAACAGAGGAAGAAATTGCTGACACTGACCT
TAAGCAAGAACAGCCTTCCGACTTAGCCAGTGCTTATGTTACTGAGGATTTAGAGTCTCCTACCATAGTACACCAAGTTC
ATCAGACAATTGATGATGAGACAATACTTATCGTTCCTTCACCACATGGCTTTATCCAGGCATCTGATGGTATAGACGCT
GAGTCTGTCTTGCCTTTGACAACACTAACAGATCCCATATTTCAACATCATCAGGAAGAATCTAATATAATTGGATCATC
TTTGGGCAGTCCTGTTTCTGAGGACTCAAAGGATGTTGAGGACTTGGTAAACTGTCAC

Alignment

ORF - retro_rnor_2871 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.75 %
• Parental protein coverage: 53.48 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RSKWLNYLNWKQSGGTEWTKEDEINLILRIAELDVADENDINWDLLAEGWSSVRSPQWLRSKWWTIKRQI
          RS...N.LNWKQSGGTEWTKEDEINLILRIAELDVADENDINWDLLAEGWSSVRSPQWLRSK.W.IKRQI
Retrocopy RSNYSN-LNWKQSGGTEWTKEDEINLILRIAELDVADENDINWDLLAEGWSSVRSPQWLRSKRWAIKRQI

Parental  ANHKDVSFPASTDSPAASVDSETITLNSGTLQTFEILPSFHLQPTGTPGTYLLQTSSSQGLPLTLTTSPT
          ANHKDVSFPASTDSPAASVDSETITLNSGTLQTFEILPSFHLQPTGTPGTYLLQTSSSQGLPLTLTTSPT
Retrocopy ANHKDVSFPASTDSPAASVDSETITLNSGTLQTFEILPSFHLQPTGTPGTYLLQTSSSQGLPLTLTTSPT

Parental  VTLAAAAPASPEQIIVHALSPEHLLNTSDNVTVQCHTPRVIIQTVATEDITSSISQAELTADSDLHSSDF
          VTLAA..PASPE.IIVHALSPEHLLNTSDNVTVQCHTPRVIIQTVATEDI.SSISQAELTADSD.HSSDF
Retrocopy VTLAA--PASPE*IIVHALSPEHLLNTSDNVTVQCHTPRVIIQTVATEDIASSISQAELTADSDFHSSDF

Parental  PEPPDALEADTFPDEIPRPKMTIQPSFNNAHVSKYSDQNSTELMNSVMVRTEEEIADTDLKQEPPSDLAS
          PEPPDALEADTFPDEIPRPKMTIQPSFNNAHVSKYSDQNSTELMNSVMVRTEEEIADTDLKQE.PSDLAS
Retrocopy PEPPDALEADTFPDEIPRPKMTIQPSFNNAHVSKYSDQNSTELMNSVMVRTEEEIADTDLKQEQPSDLAS

Parental  AYVTEDLESPTIVHQVHQTIDDETILIVPSPHGFIQASDGIDAESVLPLTTLTDPIFQHHQEESNIIGSS
          AYVTEDLESPTIVHQVHQTIDDETILIVPSPHGFIQASDGIDAESVLPLTTLTDPIFQHHQEESNIIGSS
Retrocopy AYVTEDLESPTIVHQVHQTIDDETILIVPSPHGFIQASDGIDAESVLPLTTLTDPIFQHHQEESNIIGSS

Parental  LGSPVSEDSKDVEDLVNCH
          LGSPVSEDSKDVEDLVNCH
Retrocopy LGSPVSEDSKDVEDLVNCH

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	46.66 RPM
SRP017611_kidney	0.00 RPM	22.89 RPM
SRP017611_liver	0.00 RPM	13.99 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2871 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2871 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2871 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000042508	1 retrocopy	retro_mmus_85,
Rattus norvegicus	ENSRNOG00000005908	2 retrocopies	retro_rnor_1330, retro_rnor_2871 ,