RetrogeneDB ID: retro_rnor_1330

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 18:11401895..11403086(+)
• 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_1330
ACGGAGCCAGGTGACATCGTCACACAGGGTGTGTCTTGGGCAGCTGTAGCGGAAAGAGTGGGTACCCGCTCAGAAAAGCA
ATGCCGTTCTAAATGGCTCAACTACCTGAACTGGAAACAGAGTGGGGGAACTGAGTGGACCAAGGAAGATGAAATCAATC
TCATCCTCAGGATAGCTGAGCTTGATGTAGCTGATGAAAATGACATAAACTGGGATCTTCTAGCTGAGGGATGGAGCAGT
GTTCGTTCACCACAGTGGCTTCGAAGTAAACGGTGGGCCATCAAAAGGCAAATCGCAAACCATAAGGATGTTTCGTTTCC
TGCTTCAACAGACTCCCCTGCTGCTTCTGTTGACTCAGAAACAATAACACTAAACAGTGGAACACTACAAACATTTGAGA
TTCTTCCATCTTTCCATTTACAGCCTACTGGTACTCCAGGCACCTACCTTCTTCAAACAAGCTCAAGTCAAGGCCTTCCC
CTAACACTGACCACAAGTCCCACAGTAACCCTGGCAGCTGCTGCTCCTGCTTCTCCTGAACAGATCATTGTTCATGCTTT
ATCCCCGGAACATTTGTTGAACACAAGTGACAATGTCACAGTACAGTGTCACACACCAAGAGTCATCATTCAAACTGTTG
CTACAGAGGACATCACTTCTTCAATATCCCAAGCAGAACTGACAGCTGATAGTGATCTTCATTCATCTGATTTTCCTGAG
CCTCCAGATGCACTAGAAGCAGACACTTTCCCAGATGAAATTCCTCGGCCTAAGATGACTATACAACCATCATTTAATAA
TGCTCATGTGTCTAAATACAGTGACCAAAATAGCACAGAACTGATGAATAGTGTCATGGTCAGAACAGAGGAAGAAATTG
CTGACACTGACCTTAAGCAAGAACCGCCTTCCGACTTAGCCAGTGCTTATGTTACTGAGGATTTAGAGTCTCCTACCATA
GTACACCAAGTTCATCAGACAATTGATGATGAGACAATACTTATCGTTCCTTCACCACATGGCTTTATCCAGGCATCTGA
TGGTATCGACGCTGAGTCTGTCTTGCCTTTGACAACAATAACAGATCCCATATTTCAACATCATCAGGAAGAATCGAATA
TAATTGGATCATCTTTGGGCAGTCCTGTTTCTGAGGACTCAAAGGATGTTGAGGACTTGGTAAACTGTCAC

Alignment

ORF - retro_rnor_1330 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.24 %
• Parental protein coverage: 57.54 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TEPGDIVTQGVSWAAVAERVGTRSEKQCRSKWLNYLNWKQSGGTEWTKEDEINLILRIAELDVADENDIN
          TEPGDIVTQGVSWAAVAERVGTRSEKQCRSKWLNYLNWKQSGGTEWTKEDEINLILRIAELDVADENDIN
Retrocopy TEPGDIVTQGVSWAAVAERVGTRSEKQCRSKWLNYLNWKQSGGTEWTKEDEINLILRIAELDVADENDIN

Parental  WDLLAEGWSSVRSPQWLRSKWWTIKRQIANHKDVSFPASTDSPAASVDSETITLNSGTLQTFEILPSFHL
          WDLLAEGWSSVRSPQWLRSK.W.IKRQIANHKDVSFPASTDSPAASVDSETITLNSGTLQTFEILPSFHL
Retrocopy WDLLAEGWSSVRSPQWLRSKRWAIKRQIANHKDVSFPASTDSPAASVDSETITLNSGTLQTFEILPSFHL

Parental  QPTGTPGTYLLQTSSSQGLPLTLTTSPTVTLAAAAPASPEQIIVHALSPEHLLNTSDNVTVQCHTPRVII
          QPTGTPGTYLLQTSSSQGLPLTLTTSPTVTLAAAAPASPEQIIVHALSPEHLLNTSDNVTVQCHTPRVII
Retrocopy QPTGTPGTYLLQTSSSQGLPLTLTTSPTVTLAAAAPASPEQIIVHALSPEHLLNTSDNVTVQCHTPRVII

Parental  QTVATEDITSSISQAELTADSDLHSSDFPEPPDALEADTFPDEIPRPKMTIQPSFNNAHVSKYSDQNSTE
          QTVATEDITSSISQAELTADSDLHSSDFPEPPDALEADTFPDEIPRPKMTIQPSFNNAHVSKYSDQNSTE
Retrocopy QTVATEDITSSISQAELTADSDLHSSDFPEPPDALEADTFPDEIPRPKMTIQPSFNNAHVSKYSDQNSTE

Parental  LMNSVMVRTEEEIADTDLKQEPPSDLASAYVTEDLESPTIVHQVHQTIDDETILIVPSPHGFIQASDGID
          LMNSVMVRTEEEIADTDLKQEPPSDLASAYVTEDLESPTIVHQVHQTIDDETILIVPSPHGFIQASDGID
Retrocopy LMNSVMVRTEEEIADTDLKQEPPSDLASAYVTEDLESPTIVHQVHQTIDDETILIVPSPHGFIQASDGID

Parental  AESVLPLTTLTDPIFQHHQEESNIIGSSLGSPVSEDSKDVEDLVNCH
          AESVLPLTT.TDPIFQHHQEESNIIGSSLGSPVSEDSKDVEDLVNCH
Retrocopy AESVLPLTTITDPIFQHHQEESNIIGSSLGSPVSEDSKDVEDLVNCH

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	0.07 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_1330 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1330 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1330 has 0 orthologous retrocopies within eutheria group .

---

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,