RetrogeneDB ID: retro_rnor_1141

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 15:30758908..30759241(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Gtf2a2
• Ensembl ID: ENSRNOG00000011062
• Aliases: None
• Description: Transcription initiation factor IIA subunit 2 [Source:UniProtKB/Swiss-Prot;Acc:O08950]

Sequence

>retro_rnor_1141
ATGGCATATCAGTTATGCAGAAGTACAACTTTGGGGAACAGTCTTCAAGAGAGCCTTGATGAGCTCATACAGTCTCAACA
GATCACTCCCGCCCCCAGCTTGCCCTTCAAGGTCTACTTCAGTTTGATAAAACTATAAATGCAGCATAGCATTGGCTCAG
AGAGTCAGGAACAGAGTCGATTTCAGGGACTCTCCAAATACAGATTCTGAGACAATGTTTAGACTTTTGTATTGAATGAT
GTTGAATTGAGAGAGGTGACAGAACGTATTAAAGTGGATAAAGGGAAAATTGTAGCCTGTGATGGTAAAAATACTGGCTC
CAATACTACAAAA

Alignment

ORF - retro_rnor_1141 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.29 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAYQLYRNTTLGNSLQESLDELIQSQQITPQLALQVLLQFDKA---INSALAQRVRNRVNFRGSLNTYRF
          MAYQL.R.TTLGNSLQESLDELIQSQQITP...L.....F....................F.G.L..YRF
Retrocopy MAYQLCRSTTLGNSLQESLDELIQSQQITPAPSLPFKVYFSLIKL*MQHSIGSESQEQSRFQG-LSKYRF

Parental  CDNVWTFVLNDVEFREVTELIKVDKVKIVACDGKNTGSNTTE
          .DNV.TFVLNDVE.REVTE.IKVDK.KIVACDGKNTGSNTT.
Retrocopy *DNV*TFVLNDVELREVTERIKVDKGKIVACDGKNTGSNTTK

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	8.77 RPM
SRP017611_kidney	0.00 RPM	12.42 RPM
SRP017611_liver	0.00 RPM	7.60 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1141 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1141 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1141 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000010298	1 retrocopy	retro_btau_1649,
Canis familiaris	ENSCAFG00000016665	2 retrocopies	retro_cfam_786, retro_cfam_912,
Cavia porcellus	ENSCPOG00000000816	1 retrocopy	retro_cpor_525,
Dipodomys ordii	ENSDORG00000007867	3 retrocopies	retro_dord_377, retro_dord_385, retro_dord_695,
Homo sapiens	ENSG00000140307	1 retrocopy	retro_hsap_4034,
Macaca mulatta	ENSMMUG00000018428	1 retrocopy	retro_mmul_2303,
Monodelphis domestica	ENSMODG00000011636	1 retrocopy	retro_mdom_1563,
Otolemur garnettii	ENSOGAG00000007061	1 retrocopy	retro_ogar_1752,
Ochotona princeps	ENSOPRG00000012841	1 retrocopy	retro_opri_908,
Pan troglodytes	ENSPTRG00000007129	1 retrocopy	retro_ptro_2734,
Rattus norvegicus	ENSRNOG00000011062	2 retrocopies	retro_rnor_1021, retro_rnor_1141 ,
Sorex araneus	ENSSARG00000012228	2 retrocopies	retro_sara_607, retro_sara_734,
Sus scrofa	ENSSSCG00000004583	3 retrocopies	retro_sscr_545, retro_sscr_934, retro_sscr_935,
Ictidomys tridecemlineatus	ENSSTOG00000004010	3 retrocopies	retro_itri_1631, retro_itri_440, retro_itri_925,
Tupaia belangeri	ENSTBEG00000001053	9 retrocopies	retro_tbel_1162, retro_tbel_1207, retro_tbel_123, retro_tbel_1394, retro_tbel_1439, retro_tbel_257, retro_tbel_2655, retro_tbel_2737, retro_tbel_513,
Xenopus tropicalis	ENSXETG00000022002	1 retrocopy	retro_xtro_18,