RetrogeneDB ID: retro_itri_1608

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393570.1:431535..432353(+)
• Located in intron of: ENSSTOG00000001930

Retrocopy information

• Ensembl ID: ENSSTOG00000023618
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MORF4L1
• Ensembl ID: ENSSTOG00000013294
• Aliases: None
• Description: mortality factor 4 like 1 [Source:HGNC Symbol;Acc:16989]

Sequence

>retro_itri_1608
ATACATTACAGTGGTTGGAATAAAAATTGGGAGGAATGGGTTCCAGAGAGCAGAGTGCTCAAGTACGTGGACACCAATCT
GCAGAAACAGGGAGAACTCCAAAAAGCCAATCTAGGAGCAGTATGCAGAGGGGAACATGAGAGAGGCTGCTCCAGGAAAG
AAGACATCTGGTCTGCAACAGAAAAATGTTGAAGTGAAAACCAAAAAGAACACACAGAAAACACCTGGAAATGGAGATGA
TGGTAGTACCAATGAGACACGTCAGCCTCCTCGGAAGAAAAGGGCCCAGGTAGATCCTACTGTTGAAAATGAAGAAACAT
TTATGAACATAGTTGAAGTTAAAGTAAAGATTCCTGAAGAGCTAAAACCAGGGCTTGCTGATGACTGGGACTTAATTACC
AGATAATAACAGCTCTTTTATCTTCCTCCAAGAAAAATATGGATTCTATTCTTGAGGATTATGCAAATTACAAGAAATCT
CGAGTAAACACAGATAATAAGGAGTATGTTTTTAATGAAGTTGTGGCAGGAATAAAAGAATATTTCAATGTAATGCTGGG
CACTCAGCTGCTCTACAAATTTGAGAGACCACAGTATGCTGAAATCCTTGCAGATCATCCTGATGCACCCATGTCCAGGT
GTATGGAACGCAGCATCTACTGAGATTATTTGCACGAATTGGAGCAATGTTGGCCTATACACCTCTGGATGAGAAGAGCC
TTGCTTTATTACTGAATTATCTTCATGATTTCCTCAAGTACCTGGCAAAGAATTCTGCAACTTTGTTTAGTGCCAGCAAT
TATGAAGTCATGCCTCCT

Alignment

ORF - retro_itri_1608 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.96 %
• Parental protein coverage: 75.41 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VHHPLLTSSWDEWVPESRVLKYVDTNLQKQRELQKANQ-EQYAEGKMRGAAPGKKTSGLQQKNVEVKTKK
          .H.......W.EWVPESRVLKYVDTNLQKQ.ELQKAN..EQYAEG.MR.AAPGKKTSGLQQKNVEVKTKK
Retrocopy IHYSGWNKNWEEWVPESRVLKYVDTNLQKQGELQKANL>EQYAEGNMREAAPGKKTSGLQQKNVEVKTKK

Parental  NKQKTPGNGDGGSTSETPQPPRKKRARVDPTVENEETFMNRVEVKVKIPEELKPWLVDDWDLITRQKQLF
          N.QKTPGNGD.GST.ET.QPPRKKRA.VDPTVENEETFMN.VEVKVKIPEELKP.L.DDWDLITR..QLF
Retrocopy NTQKTPGNGDDGSTNETRQPPRKKRAQVDPTVENEETFMNIVEVKVKIPEELKPGLADDWDLITR**QLF

Parental  YLP-AKKNVDSILEDYANYKKSRGNTDNKEYAVNEVVAGIKEYFNVMLGTQLLYKFERPQYAEILADHPD
          YLP..KKN.DSILEDYANYKKSR.NTDNKEY..NEVVAGIKEYFNVMLGTQLLYKFERPQYAEILADHPD
Retrocopy YLP<SKKNMDSILEDYANYKKSRVNTDNKEYVFNEVVAGIKEYFNVMLGTQLLYKFERPQYAEILADHPD

Parental  APMS-QVYGAPHLLRLFVRIGAMLAYTPLDEKSLALLLNYLHDFLKYLAKNSATLFSASDYEVAPP
          APMS.QVYG..HLLRLF.RIGAMLAYTPLDEKSLALLLNYLHDFLKYLAKNSATLFSAS.YEV.PP
Retrocopy APMS<QVYGTQHLLRLFARIGAMLAYTPLDEKSLALLLNYLHDFLKYLAKNSATLFSASNYEVMPP

Legend:

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

Expression

RNA-Seq

Ictidomys tridecemlineatus was not studied using RNA-Seq expression data.

ChIP-Seq

Ictidomys tridecemlineatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_itri_1608 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1608 was not experimentally validated.

Homology

Retrocopy orthology:

Ictidomys tridecemlineatus 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 28 parental genes, and 72 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012344	1 retrocopy	retro_amel_124,
Bos taurus	ENSBTAG00000010988	1 retrocopy	retro_btau_137,
Canis familiaris	ENSCAFG00000014113	1 retrocopy	retro_cfam_20,
Callithrix jacchus	ENSCJAG00000002214	5 retrocopies	retro_cjac_2113, retro_cjac_2280, retro_cjac_2574, retro_cjac_3026, retro_cjac_3179,
Cavia porcellus	ENSCPOG00000003778	3 retrocopies	retro_cpor_114, retro_cpor_1409, retro_cpor_915,
Equus caballus	ENSECAG00000008091	1 retrocopy	retro_ecab_62,
Felis catus	ENSFCAG00000012197	1 retrocopy	retro_fcat_75,
Homo sapiens	ENSG00000185787	3 retrocopies	retro_hsap_309, retro_hsap_3125, retro_hsap_850,
Gorilla gorilla	ENSGGOG00000016826	3 retrocopies	retro_ggor_125, retro_ggor_2141, retro_ggor_694,
Loxodonta africana	ENSLAFG00000009851	1 retrocopy	retro_lafr_62,
Myotis lucifugus	ENSMLUG00000001756	1 retrocopy	retro_mluc_324,
Macaca mulatta	ENSMMUG00000022926	1 retrocopy	retro_mmul_1064,
Monodelphis domestica	ENSMODG00000011517	2 retrocopies	retro_mdom_150, retro_mdom_158,
Mustela putorius furo	ENSMPUG00000015429	1 retrocopy	retro_mputfur_180,
Mus musculus	ENSMUSG00000062270	9 retrocopies	retro_mmus_1454, retro_mmus_1697, retro_mmus_176, retro_mmus_1771, retro_mmus_1825, retro_mmus_1833, retro_mmus_2500, retro_mmus_2612, retro_mmus_289,
Nomascus leucogenys	ENSNLEG00000008678	3 retrocopies	retro_nleu_417, retro_nleu_445, retro_nleu_51,
Oryctolagus cuniculus	ENSOCUG00000015117	2 retrocopies	retro_ocun_108, retro_ocun_21,
Otolemur garnettii	ENSOGAG00000006047	4 retrocopies	retro_ogar_1594, retro_ogar_2616, retro_ogar_2896, retro_ogar_50,
Pongo abelii	ENSPPYG00000006703	4 retrocopies	retro_pabe_1046, retro_pabe_201, retro_pabe_2581, retro_pabe_695,
Pan troglodytes	ENSPTRG00000007351	3 retrocopies	retro_ptro_2114, retro_ptro_47, retro_ptro_591,
Rattus norvegicus	ENSRNOG00000014410	6 retrocopies	retro_rnor_1076, retro_rnor_2270, retro_rnor_2357, retro_rnor_374, retro_rnor_793, retro_rnor_980,
Sorex araneus	ENSSARG00000004519	1 retrocopy	retro_sara_15,
Sarcophilus harrisii	ENSSHAG00000018402	1 retrocopy	retro_shar_393,
Sus scrofa	ENSSSCG00000001769	1 retrocopy	retro_sscr_93,
Ictidomys tridecemlineatus	ENSSTOG00000013294	3 retrocopies	retro_itri_111, retro_itri_1545, retro_itri_1608 ,
Tupaia belangeri	ENSTBEG00000001897	8 retrocopies	retro_tbel_1694, retro_tbel_1704, retro_tbel_4638, retro_tbel_518, retro_tbel_550, retro_tbel_69, retro_tbel_753, retro_tbel_76,
Tursiops truncatus	ENSTTRG00000016606	1 retrocopy	retro_ttru_472,
Vicugna pacos	ENSVPAG00000008847	1 retrocopy	retro_vpac_229,