RetrogeneDB ID: retro_shar_25

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL849915.1:2380619..2381198(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSHAG00000016852
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: ARF3
• Ensembl ID: ENSSHAG00000003635
• Aliases: None
• Description: ADP-ribosylation factor 3 [Source:HGNC Symbol;Acc:654]

Sequence

>retro_shar_25
ATGGGGACCTGGAACTCTAAATCCTCCAAGGTCAAGCAGGCCCGAGTTCTGCTCTTGGGACTGGATTTCTCAGGGAAGTC
AACCATCCTTTACAAATTAAAGCGCATCAAGGACTTCACAACCATCCCGACCATCGGCTTCAATGTGGAAATGATAGAGA
CGGAGAAAAATATTAATCTCACGGTCTGGGACGTTGGAGGGCAGTCCCAGATGAGGAGCCTGTGGGACCATTACTGTGAG
AATACAGATGTGCTGGTCTATGTGGTGGACAGCACCGACCAGAAGCAGCTGGAGGCCTCCCGCAGGGAATTCGAGCTCAT
CCTGAAGAACGAGCACATCAGGAATGTGCCCGTGGTGCTGCTAGCCAACAAGCAAGACCTGCCCGGGGCTTTCACGGCGG
AAGATATCACCAGGAAATTCAAGATGAAGAAAAATTGTGGAGACCGGGACTGGTACGTCCAGCCTTGCTGTGCCATCTCG
GGAGATGGCCTGGCTGATGGCTTCAAGAAAGTGACCGAGTTCATCCAGAGATACAGGAACTCTGCAGAAGCAACTTGGGC
CTTCTTCAGGCAGAATTAA

Alignment

ORF - retro_shar_25 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.64 %
• Parental protein coverage: 82.35 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KEMRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEY-KNISFTVWDVGGQDKIRPLWRHYFQN
          K..R.L..GLD..GK.TILYKLK.....TTIPTIGFNVE..E..KNI..TVWDVGGQ...R.LW.HY..N
Retrocopy KQARVLLLGLDFSGKSTILYKLKRIKDFTTIPTIGFNVEMIETEKNINLTVWDVGGQSQMRSLWDHYCEN

Parental  TQGLIFVVDSNDRERVNEAREELMRMLAEDELRDAVLLVFANKQDLPNAMNAAEITDKLGL-HSLRHRNW
          T..L..VVDS.D.......R.E....L.....R.......ANKQDLP.A..A..IT.K.........R.W
Retrocopy TDVLVYVVDSTDQKQLEASRREFELILKNEHIRNVPVVLLANKQDLPGAFTAEDITRKFKMKKNCGDRDW

Parental  YIQATCATSGDGLYEG
          Y.Q..CA.SGDGL..G
Retrocopy YVQPCCAISGDGLADG

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Sarcophilus harrisii was not studied using RNA-Seq expression data.

ChIP-Seq

Sarcophilus harrisii was not studied using ChIP-Seq data.

EST

Sarcophilus harrisii was not studied using EST data.

TSS

Sarcophilus harrisii was not studied using FANTOM5 data.

Lab

retro_shar_25 was not experimentally validated.

Homology

Retrocopy orthology:

Sarcophilus harrisii does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

---

Parental genes homology:

Parental genes homology involve 18 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000008240	1 retrocopy	retro_acar_12,
Cavia porcellus	ENSCPOG00000025074	1 retrocopy	retro_cpor_92,
Ciona savignyi	ENSCSAVG00000007011	1 retrocopy	retro_csav_2,
Homo sapiens	ENSG00000134287	1 retrocopy	retro_hsap_36,
Latimeria chalumnae	ENSLACG00000019009	1 retrocopy	retro_lcha_10,
Loxodonta africana	ENSLAFG00000004207	1 retrocopy	retro_lafr_115,
Macropus eugenii	ENSMEUG00000005072	7 retrocopies	retro_meug_1036, retro_meug_1117, retro_meug_1857, retro_meug_29, retro_meug_395, retro_meug_616, retro_meug_946,
Microcebus murinus	ENSMICG00000017545	1 retrocopy	retro_mmur_37,
Monodelphis domestica	ENSMODG00000013804	1 retrocopy	retro_mdom_241,
Mus musculus	ENSMUSG00000051853	1 retrocopy	retro_mmus_147,
Nomascus leucogenys	ENSNLEG00000017859	2 retrocopies	retro_nleu_1348, retro_nleu_94,
Petromyzon marinus	ENSPMAG00000000531	1 retrocopy	retro_pmar_5,
Rattus norvegicus	ENSRNOG00000033155	1 retrocopy	retro_rnor_272,
Rattus norvegicus	ENSRNOG00000048089	1 retrocopy	retro_rnor_2521,
Sarcophilus harrisii	ENSSHAG00000003635	2 retrocopies	retro_shar_25 , retro_shar_364,
Sarcophilus harrisii	ENSSHAG00000014599	3 retrocopies	retro_shar_106, retro_shar_462, retro_shar_725,
Tetraodon nigroviridis	ENSTNIG00000011685	1 retrocopy	retro_tnig_19,
Tursiops truncatus	ENSTTRG00000004698	1 retrocopy	retro_ttru_1081,