RetrogeneDB ID: retro_dnov_1561

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_23499:49428..49951(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL7
• Ensembl ID: ENSDNOG00000017654
• Aliases: None
• Description: ribosomal protein L7 [Source:HGNC Symbol;Acc:10363]

Sequence

>retro_dnov_1561
AAAGAGAAGGAGAAGGTTCCTGCTATGCCAGAAACCCTTCAGGAAAAGCAAAGGAATTTTGCTGAACTGAAGATCAAGCA
TTTGAGAAGGAAGTTTGCCCAAAAGATGCTTTGAAAGGCAAGAAGGAAGCTTACCTATGAAAAAGCTTAAGCACTAGCAC
ATGGAATACAGGCAGATGTACAGGACTGAGATTCAAATAGCTAGAATGGCAAGAAAAGCTGGCAACTTCTATGTACCTGT
GGAACCCAAATTGGCATTTGTCATCAGGATCAGAGGTATCAACGGTGTGAGCCCAAAGGTCTGAAAAGTGTTACAGCTTC
TTTGCCTTTGCCAGATCTTCAATGGCAGCTTTGTTAAGTTCAACAAGGCCTCAATTAACATGCTGAGAATTGTGGAATCA
TATATCGCATTGGGGTACCCGAACCTGAAGTCAGTGAATGAACTGATCTGTAAGCGTGGTTATGGCAAAATAAACAAGAA
GTGGATTGCCCTGACAGGTAACTCATTGATTGCATGATCTCTT

Alignment

ORF - retro_dnov_1561 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.0 %
• Parental protein coverage: 92.55 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EKKKKVPAVPETLKKKRRNFAELKIKRLRKKFAQKMLRKARRKLIYEKA-KHYHKEYRQMYRTEIRMARM
          ..K.KVPA.PETL..K.RNFAELKIK.LR.KFAQKML.KARRKL.YEKA.KH.H.EYRQMYRTEI..ARM
Retrocopy KEKEKVPAMPETLQEKQRNFAELKIKHLRRKFAQKML*KARRKLTYEKA>KH*HMEYRQMYRTEIQIARM

Parental  ARKAGNFYVPAEPKLAFVIRIRGINGVSPKVRKVLQLLRLRQIFNGTFVKLNKASINMLRIVEPYIAWGY
          ARKAGNFYVP.EPKLAFVIRIRGINGVSPKV.KVLQLL.L.QIFNG.FVK.NKASINMLRIVE.YIA.GY
Retrocopy ARKAGNFYVPVEPKLAFVIRIRGINGVSPKV*KVLQLLCLCQIFNGSFVKFNKASINMLRIVESYIALGY

Parental  PNLKSVNELIYKRGYGKINKKRIALTDNSLIARSL
          PNLKSVNELI.KRGYGKINKK.IALT.NSLIA.SL
Retrocopy PNLKSVNELICKRGYGKINKKWIALTGNSLIA*SL

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
SRP012922_ascending_colon	0.39 RPM	220.92 RPM
SRP012922_cerebellum	0.27 RPM	120.56 RPM
SRP012922_heart	0.00 RPM	123.90 RPM
SRP012922_kidney	0.00 RPM	273.80 RPM
SRP012922_liver	0.00 RPM	112.70 RPM
SRP012922_lung	0.00 RPM	262.23 RPM
SRP012922_quadricep_muscle	0.00 RPM	188.66 RPM
SRP012922_spleen	0.00 RPM	342.58 RPM

ChIP-Seq

Dasypus novemcinctus was not studied using ChIP-Seq data.

EST

Dasypus novemcinctus was not studied using EST data.

TSS

Dasypus novemcinctus was not studied using FANTOM5 data.

Lab

retro_dnov_1561 was not experimentally validated.

Homology

Retrocopy orthology:

Dasypus novemcinctus 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.

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 94 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001821	5 retrocopies	retro_amel_1230, retro_amel_1632, retro_amel_760, retro_amel_933, retro_amel_937,
Canis familiaris	ENSCAFG00000008021	28 retrocopies	retro_cfam_1039, retro_cfam_1075, retro_cfam_1079, retro_cfam_1167, retro_cfam_1209, retro_cfam_1236, retro_cfam_1270, retro_cfam_1308, retro_cfam_1390, retro_cfam_1436, retro_cfam_1445, retro_cfam_1453, retro_cfam_1524, retro_cfam_1541, retro_cfam_1699, retro_cfam_1755, retro_cfam_1855, retro_cfam_1856, retro_cfam_2051, retro_cfam_2192, retro_cfam_338, retro_cfam_403, retro_cfam_563, retro_cfam_609, retro_cfam_737, retro_cfam_74, retro_cfam_922, retro_cfam_998,
Dasypus novemcinctus	ENSDNOG00000013485	1 retrocopy	retro_dnov_689,
Dasypus novemcinctus	ENSDNOG00000017654	15 retrocopies	retro_dnov_1561 , retro_dnov_1692, retro_dnov_182, retro_dnov_1893, retro_dnov_209, retro_dnov_2158, retro_dnov_2568, retro_dnov_264, retro_dnov_2657, retro_dnov_279, retro_dnov_287, retro_dnov_365, retro_dnov_655, retro_dnov_77, retro_dnov_971,
Felis catus	ENSFCAG00000028446	6 retrocopies	retro_fcat_1643, retro_fcat_230, retro_fcat_255, retro_fcat_338, retro_fcat_342, retro_fcat_945,
Latimeria chalumnae	ENSLACG00000003571	1 retrocopy	retro_lcha_63,
Loxodonta africana	ENSLAFG00000017110	10 retrocopies	retro_lafr_140, retro_lafr_169, retro_lafr_334, retro_lafr_462, retro_lafr_47, retro_lafr_524, retro_lafr_694, retro_lafr_707, retro_lafr_816, retro_lafr_909,
Macropus eugenii	ENSMEUG00000016319	9 retrocopies	retro_meug_1002, retro_meug_1449, retro_meug_1942, retro_meug_1947, retro_meug_60, retro_meug_760, retro_meug_84, retro_meug_968, retro_meug_99,
Monodelphis domestica	ENSMODG00000007136	4 retrocopies	retro_mdom_1341, retro_mdom_1998, retro_mdom_371, retro_mdom_66,
Oryctolagus cuniculus	ENSOCUG00000008407	12 retrocopies	retro_ocun_109, retro_ocun_1164, retro_ocun_1282, retro_ocun_1342, retro_ocun_1494, retro_ocun_1646, retro_ocun_1879, retro_ocun_456, retro_ocun_501, retro_ocun_718, retro_ocun_727, retro_ocun_785,
Sus scrofa	ENSSSCG00000006182	3 retrocopies	retro_sscr_1138, retro_sscr_209, retro_sscr_796,