RetrogeneDB ID: retro_mmus_1210

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 14:56415642..56416503(+)
• Located in intron of: ENSMUSG00000000365

Retrocopy information

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

Parental gene information

• Parental gene symbol: Atf7ip2
• Ensembl ID: ENSMUSG00000039200
• Aliases: Atf7ip2, 4930558K11Rik, BC018510, Get-1, PSM2
• Description: activating transcription factor 7 interacting protein 2 [Source:MGI Symbol;Acc:MGI:1922579]

Sequence

>retro_mmus_1210
ATGGAAAGTCCAGACAGAAAAAGACAGAAGGTTTTAAAGGCCAAGAAAACAATGCCTACAAGTTACCAGAAGCAGTTGGA
GATCCTGAACAAGTCAACGAATGTTGAAGCTCCAAAAACAACAGTTGGAACTAATATTCCAAATGGCCATAATCAGAAGA
TGTTTTCAAAAAACAAAGAAAATGTTAAGGTCATGAAAGCTTCAGAGCAAATTAATGAAAATACTTGTGAGGCTCTGGAA
AGACATACAGCACTGCTAGAACAGGTTAAACATTGGATTCGACAGGAGATCTGCATGATAAACTGTAATTTATTTGATAA
AAAACTGAATGAATTGAATGAACGCATTGGGAAGACCCAGTGCAAGAGTAGACATGAAGCAATAGCTGGTGAACTCTTTG
TAAAAATAAGAAGACTTCAAAAACGCATCAAAACAGTATTATCATCTCAAAGAAATTGTTTGGAACCAAACACATTACCC
AGTAATACAGTCTGTAAGGTTACAGATTCAGAGGCTATGAATTTGAATGTGACCCAAAAGTCAGTTAAAAGTCGAAGTAA
AAGAATATCTTCTGTGAACCATACCCCTTTAAACTCTTCAGAAAAAGCAGGTAGAAAGACTAATTTGCCATCAACTTGTG
TTGAGTTTGCTTCTGAAAGTAACACTAATGATGTTATGTTGATTTCTGTGAAAAATCCTAATTTGACAACTTCAATTACA
TCAGATCAAACAGAAATTAGAAAAAATACATCAAGAAATTTGAGCATCTCACCTAATAGCATGATTAAAGTTGGGCCCGT
AGAGAAGAAATTTGATTTTGTTATTGACTTGACAAGAGAAGGCCCGTCCAACTACAGCATA

Alignment

ORF - retro_mmus_1210 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.56 %
• Parental protein coverage: 63.5 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MESPDRKRQKVLKAKKTMPTSYQKQLEILNKSTNVEAPKTTVGTNIPNGHNQKMFSKNKENVKVMKVSEQ
          MESPDRKRQKVLKAKKTMPTSYQKQLEILNKSTNVEAPKTTVGTNIPNGHNQKMFSKNKENVKVMK.SEQ
Retrocopy MESPDRKRQKVLKAKKTMPTSYQKQLEILNKSTNVEAPKTTVGTNIPNGHNQKMFSKNKENVKVMKASEQ

Parental  INENACGALERHTALLEQVKHWIRQEICMINCNLFDKKLNELNERIGKTQCKSRHEAIAGELFVKIRRLQ
          INEN.C.ALERHTALLEQVKHWIRQEICMINCNLFDKKLNELNERIGKTQCKSRHEAIAGELFVKIRRLQ
Retrocopy INENTCEALERHTALLEQVKHWIRQEICMINCNLFDKKLNELNERIGKTQCKSRHEAIAGELFVKIRRLQ

Parental  KRIKTVLSSQRNCLEPNTLPSNTVCKVTDSEAMNLNVTQKSVKSRSKRISSVNHTPLNSSEKAGRKTNLP
          KRIKTVLSSQRNCLEPNTLPSNTVCKVTDSEAMNLNVTQKSVKSRSKRISSVNHTPLNSSEKAGRKTNLP
Retrocopy KRIKTVLSSQRNCLEPNTLPSNTVCKVTDSEAMNLNVTQKSVKSRSKRISSVNHTPLNSSEKAGRKTNLP

Parental  STCVEFASESNTDDVMLISVKNSNLTTSITSEQTEIRKNTSRNLSNSPNSMIKVGPVEKKFDFVIDLTRE
          STCVEFASESNT.DVMLISVKN.NLTTSITS.QTEIRKNTSRNLS.SPNSMIKVGPVEKKFDFVIDLTRE
Retrocopy STCVEFASESNTNDVMLISVKNPNLTTSITSDQTEIRKNTSRNLSISPNSMIKVGPVEKKFDFVIDLTRE

Parental  GPSNYSI
          GPSNYSI
Retrocopy GPSNYSI

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	0.00 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.40 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.73 RPM	12.62 RPM

ChIP-Seq

RNA Polymerase II activity may be related with retro_mmus_1210 in 1 libraries

ENCODE library ID	Target	ChIP-Seq Peak coordinates
ENCFF001YKA	POLR2A	14:56415024..56415120

EST

No EST(s) were mapped for retro_mmus_1210 retrocopy.

TSS

No TSS is located nearby retro_mmus_1210 retrocopy 5' end.

Lab

retro_mmus_1210 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1210 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000039200	1 retrocopy	retro_mmus_1210 ,